This is actually a standard property of the homotopy category of complexes on which construction of the derived category is based, formulated in unusual way.
For a quasi-isomorphism $s:X'\to X$ and $f\in Hom(X',Y)$ denote by $fs^{-1}$ the image of $f$ in the first colimit(in a second we will justify the choice of notation). By description of the filtered colimit, two images $fs^{-1}$ and $gt^{-1}$(for $t:X''\to X,g\in Hom(X'',Y)$) coincide iff there exists $X'''$ and qisms $p:X'''\to X',q:X'''\to X''$ and a map $r\in Hom(X''',Y)$ such that $sp=tq,fp=gq$. This is exactly the condition for fractions $fs^{-1}$ and $gt^{-1}$ to be equivalent in the right localization by qisms(see e.g. Weibel, 10.3).
Analogously, the third colimit can be identified with the set of equivalence classes of left fractions. Now, Ore conditions guarantee that these two sets of equivalence classes coincide, which is precisely the isomorphism you are looking for.
TheEdit: As Denis-Charles Cisinski explains, the answer to the question B is just a formal consequence(thoughnegative. Indeed, I don't think that this is indeed internal Hom for arbitrary categorylet's pick a non-zero object $A$ in $C$ and consider, for category of modules over a ring it is): forgetful functor from abelian groups to setsinstance, $X=A[0], Y=A\xrightarrow{1} A$ where $Y$ is fully faithfula contractible complex concentrated in degrees $-1,0$. The second and commutes with filteredthird colimits, so arrows in the last diagram are isomorphisms already onzero as the levelcategory of complexesquasi-isomorphisms $Y\to Y'$ has a final object $Y\to 0$.
Edit: Let me add some details on But the last argument. I will prove that these are actually isomorphisms of complexes. First, let's prove itfirst colimit is not zero: for $Hom^0$. Applying forgetful functor $AB\to Sets$ we obtain the diagram from the part A because this forgetful functor commutes with filtered colimits. As it$X'=X$ there is faithful, it follows that arrowsa non-zero element $Id_A\in Hom(A,A)=Hom^0(X,Y)$ which survives in the part B are indeed isomorphisms of abelian groups. Next, we get the same for whole complexes repeating this argumentcolimit because for a quasi-isomorphism $X,Y[i]$$X'\to X$ the map $(X')^0\to A$ has to be non-zero.