You've raised a number of good questions, one of which is to better understand the graded-geometric aspects of having a boundary operation. I will try to address this part of your question, but I will begin with an apology: yours is largely a "why" question, whereas I will give only a "what" answer, motivated only after you have decided that chain complexes, etc., are useful. Also, my answer will be a bit long and rambly, and will probably raise more questions than it answers.
Notation: graded always means $\mathbb Z$-graded, with the Koszul signs (which I do not have a good way to motivate right now). Eventually I will stop even saying "graded": if I say "vector space" or "commutative algebra" or whatever, I probably mean "in the category of graded ...". Also, "vector space" almost certainly always means "abelian group" or "$R$-module" for your favorite commutative ring $R$, or ...
First, I don't know what your favorite conventions are: do you prefer that a chain complex have $\partial$ increasing or decreasing degree? Well, no matter. Let $\mathfrak Q$ denote the line ($\otimes$-invertible object) in degree $\pm 1$, so that a chain complex structure on a graded vector space $V$ includes a map of graded vector spaces $\mathfrak Q \to \operatorname{End}(V)$. (I use Q because it is the first letter of the word "homology".) Then $\mathfrak Q$ has an abelian group structure, given by $+$, and its Lie algebra is the vector space $\mathfrak Q$ with the trivial bracket. We've seen already that a chain complex is the same as a representation of the Lie algebra $\mathfrak Q$. Because this Lie algebra acts nilpotently on all representations, any such action integrates to an action of the group $\mathfrak Q$. So you can equivalently describe chain complexes as the representations of a group.
Let me describe this group a bit more. First, it is a group where? I'd like to be able to talk about "$+$ is a group structure on the set of points in $\mathfrak Q$", but that's nonsense. Instead, let $R$ be any (graded) commutative ring. Then there is a presheaf on affine schemes that assigns to $R$ the set of elements of $R$ which are homogeneous for the $\mathbb Z$-grading with grading $\mp 1$; i.e. this is the set of maps of graded vector spaces $\mathfrak Q^{\otimes -1} \to R$, where $\mathfrak Q^{\otimes -1}$ is the vector space which is $\otimes$-inverse to $\mathfrak Q$. This presheaf is in fact an affine scheme, because we have a "free" functor $\operatorname{Sym}$ from vector spaces to commutative rings: its represented by the commutative ring consisting of polynomials in one variable $\mathfrak q$, where $\mathfrak q$ has the grading of a basis element of $\mathfrak Q^{-1}$. Just to confuse notation, I will write $\mathfrak Q$ for both the invertible vector space above, and also for $\mathfrak Q = \operatorname{Spec}(\mathbb Z[\mathfrak q])$. Note that I do mean to impose that $\mathfrak q^2 = 0$, which follows from the grading of $\mathfrak q$ if $2$ is invertible in $\mathbb Z$. (So really I would be happiest picking a field of characteristic $0$, and replacing $\mathbb Z$ with that field.) Anyway, the affine scheme $\mathfrak Q$ is in fact an affine algebraic group. As a group scheme, it is the scheme that assigns to a commutative ring $R$ not just the set of grading-$(\mp 1)$ elements, but the abelian group of those (with $+$); as a Hopf algebra, the group structure is encoded by the comultiplication $\mathfrak q \mapsto 1\otimes \mathfrak q + \mathfrak q \otimes 1$.
Can we recognize this group $\mathfrak Q$ as arising from topology? No. Indeed, for any topological space $X$, its cohomology is supported entirely on the side of grading-$0$ that the vector space $\mathfrak Q$ is on, whereas the coordinate $\mathfrak q$ then has the opposite grading. In particular, the scheme $\mathfrak Q$ is inditinguishable from the trivial scheme when tested against the cohomology rings of spaces.
Nevertheless, it is tempting to try to describe $\mathfrak Q$ in topological language. The temptation comes, in part, from a famous theory of Quillen and Sullivan, which says that (not too large) toplogical spaces, if you can only see them "rationally", are the same as affine schemes over $\mathbb Q$. So henceforth I will work over the rational numbers, and wish that I hadn't picked the letter Q above. Oh, well, that's what fonts are for. (There are many conditions necessary to make the equivalence precise, and most of my examples will not satisfy those conditions, but c'est la vie.)
Let $G$ be a group. Then it has a classifying space $\mathrm B G$, with the property that $\pi_n(\mathrm B G) = \pi_{n-1} G$, and with a distinguished point $\ast \to \mathrm B G$. In general, $\mathrm B G$ has no group structure left over (the group structure on $G$ has been "used up" to create the classifying space). If instead of saying "group" I had said "homotopy-associative group", which is the correct notion of "group" in Spaces, then I would go on to describe "homotopy-$E_n$ groups", and observe that if $G$ has a homotopy-$E_n$ group structure, then $\mathrm B G$ has a homotopy-$E_{n-1}$ structure. (In particular, a (homotopy) $E_0$-structure on a space $X$ is the same as a distinguished map $\ast\to X$.) Rather than describing this theory, let me simply observe that if $G$ is a commutative group, then $\mathrm B G$ also has a commutative group structure.
Let's work rationally, and let $\mathbb G_a$ denote the additive group of the ground field $\mathfrak k$. Then there's a sequence of abelian groups $\mathrm B^n \mathbb G_a$, with $\pi_m \mathrm B^n \mathbb G_a =\mathbb G_a$ when $m=n$, and $=0$ otherwise. You already know some of these groups. In particular, the circle $S^1$ is (integrally!) a $\mathrm K(\mathbb Z,1)$, and so rationally $S^1 = \mathrm K(\mathbb G_a,1)$, since $\mathbb G_a = \mathbb G_a \otimes \mathbb Z$; so $S^1 = \mathrm B \mathbb G_a$. In general, if memory serves, $\mathrm B^n\mathbb G_a$ is the $n$-sphere, since I'm working rationally. (Yes, the $n$-sphere is a group.)
Anyway, our group $\mathfrak Q$ has homotopy only in grading $-1$: it is a "rational $-1$-sphere". This is what I meant when I said that it cannot arrise from topology: it has homotopy groups in negative spots. (So if I were clever, I would have insisted on homological grading, whence differentials go down, and $\mathfrak Q$ is the line supported in grading $-1$, and the coordinate $\mathfrak q$ has grading $+1$; then all conventions would be consistent.) We want to write $\mathfrak Q = \mathrm B^{-1}\mathbb G_a$. Well, what functor is inverse to $\mathrm B$? It's the functor of taking based loops: $\mathfrak Q = \Omega \mathbb G_a$.
In fact, by working with graded (or dg) schemes over $\mathbb k\supseteq Q$, you can realize this equation. Let $\ast \to X$ be a pointed space. The based loop space of $X$ is the homotopy pullback:
$$ \begin{matrix} \Omega X & \to & \to & \ast \\
\downarrow & \ulcorner & & \downarrow \\
\downarrow & & & \downarrow \\
\ast & \to & \to & X \end{matrix}$$
I.e. "the intersection of the point with itself".
Working instead with affine schemes, we replace the space $X$ with its ring of functions $\mathcal O(X)$, and the point $\ast$ with $\mathbb k = \mathcal O(\ast)$, and then the map $\ast \to X$ is an augmentation of $\mathcal O(X)$. Recall that the pushout of commutative rings is the tensor product; the homotopy pushout is the derived tensor product, and so we have:
$$ \Omega X = \operatorname{Spec}( \mathbb k \otimes_{\mathcal O(X)} \mathbb k) $$
where $\otimes$ means the derived tensor product.
In our case, $X = \mathbb G_a$ and $\mathcal O(X) = \mathbb k[x]$, where $x$ is a grading-$0$ coordinate function. Then you can check that, sure enough, the derived tensor product is represented by the ring $\mathbb k[\mathfrak q]$. So in some algebraic sense we do have $\mathfrak Q = \mathrm B^{-1}\mathbb G_a$.
Conversely, what I'm saying that $\mathbb G_a = \mathrm B \mathfrak Q$. You had originally asked for a deeper understanding of chain complexes, and we agreed that (at least rationally) chain complexes were $\mathfrak Q$-representations. But these are the same as sheaves of vector bundles over $\mathrm B \mathfrak Q$, which we now recognize (if we are willing to restrict ourselves only to work over $\mathbb k \subseteq \mathbb Q$) as (the underlying space of) the group $\mathbb G_a$, which is to say the affine line.
Then again, I'm not sure what to make of this, in part because everything I've said in the last few paragraphs is technically false: Quillen and Sullivan's rational homotopy theory only really starts to work when you restrict yourself to rings and spaces that only have homotopy starting in degree $2$.
Here are a few more things to think about. From the picture of "chain complexes are representations of some particular group $\mathfrak Q$", it makes sense why you might care about "chain complexes up to homotopy": that's like deciding to care only about the quotient of any given $\mathfrak Q$-representation by the $\mathfrak Q$-action (but because we're in the 21st century, there are good ways to take this quotient).
It does continue to amaze me that this group is enough to do all sorts of other parts of derived geometry. For example, let $\mathfrak g$ be a Lie algebra over $\mathbb k \subseteq \mathbb Q$, and use the same notation for the formal group with Lie algebra $\mathfrak g$ (one way to define this formal group is to take the universal enveloping algebra of $\mathfrak g$, which is ind-finite if $\mathfrak g$ is finite-dimensional, and take its "filtered dual" and thereby build a profinite commutative ring; Spec of this ring is one thing I could mean by "the formal group"). Then there is a space $\mathrm B \mathfrak g$, whose sheaves are all $\mathfrak g$-modules. This space can be equivalently described by shifting $\mathfrak g$ up one degree in homological grading, and then giving it an interesting action by $\mathfrak Q$; $\mathrm B \mathfrak g$ is the "quotient" of this action. From this perspective, the functor that turns a $\mathfrak g$-representation $V$ into a sheaf over $\mathrm B\mathfrak g$, and then takes the total space of this sheaf; that functor just is taking the quotient of the representation by the $\mathfrak g$-action. But the total space is just $V \times \mathrm B \mathfrak g$, and the $\mathfrak g$-action on $V$ is encoded by a $\mathfrak Q$-action on $V \times \mathrm B \mathfrak g$ covering the $\mathfrak Q$-action on $\mathrm B \mathfrak g$. So all stacks of the form "space mod Lie algebra action" can be encoded as "(graded) space mod $\mathfrak Q$-action". (Note: you cannot encode discrete groups this way. The $\mathfrak Q$-action only sees the infinitesimal part of the $\mathfrak g$-action, but since I'm using the formal group, and not, say, the connected simply-connected Lie group, there really is only infinitesimal action.)