Simple group of order 360
Another good example of an almost square simple group
is the alternating group $A_6$ of order $360=19^2-1$.
In order to check that the set $A$ below is an almost square root of $A_6$,
you can use the following GAP commands:
g:=AlternatingGroup(6);;
A:=[(1,2)(3,4),(1,3)(5,6),(1,2,3,4)(5,6),(1,2,3),(1,3,4),
(1,2)(3,4,5,6),(1,2)(3,4,6,5),(1,2,3,4,5),(1,2,3,4,6),
(1,2,5)(3,4,6),(1,2,5,3,4),(1,2,5,6)(3,4),(1,2,5,6,3),
(1,2,6)(3,4,5),(1,2,6,3,4),(1,2,6,5)(3,4),(1,2,6,5,3),
(1,3,4,5,6),(1,3,4,6,5)];;
Size(A);
prod:=[];;
for a in A do for b in A do Add(prod,a*b);od;od;
Size(AsSet(prod));
Note that the subset
$$
V=\{(1,2)(3,4),(1,3)(5,6),(1,2,3,4)(5,6),(1,2,3),(1,3,4)\}\subset A
$$
is an almost square root of a group isomorphic to the symmetric group $S_4$.
The set $V$ is an initial set from which our algorithm starts.
We next consider the following three 5-element subsets of $A_6$:
\begin{eqnarray*}
V_1&=&\{(1,2)(3,4),(1,3)(5,6),(1,2,3,4)(5,6),(1,2,3),(1,3,4)\},\\
V_2&=&\{(1,2)(3,4),(1,3)(5,6),(1,2,3,4)(5,6),(1,3,2),(2,3,4)\},\\
V_3&=&\{(1,2)(3,4),(1,3)(5,6),(1,2,3,4)(5,6),(1,4,2),(2,4,3)\}.
\end{eqnarray*}
Each of these subsets has the following three properties:
(1) $V_i$ is an almost square root of a group isomorphic to $S_4$;
(2) $V_i$ has a subset with three elements which is an almost square
root of a group isomorphic to the dihedral group $D_4$ of order 8;
(3) $V_i$ contains two elements of order 2.
It turns out that any 5-subset of $A_6$
with these three properties is conjugate
to one of $V_i$ or $V_i^{-1}$ under the group Aut$(A_6)$.
Each set $V_i$ is complemented to an almost square root of $A_6$.
Groups of odd order
It seems to me that the answer to Problem 3' is negative.
Proposition.
Any group of order $675$ is not an almost squared group.
Proof.
This is a straightforward consequence of Lemmas 1 and 2.
Lemma 1.
Let $G$ be a group of odd order and $|G|>3$.
If $G$ has an almost square root, then $Z(G)=\{e\}$.
Proof.
Let $A$ be an almost square root of $G$.
Then there exists exactly one element $x\in G$
which can be represented as the product $x=ab$, $a,\,b\in A$ in exactly two ways.
We will call this element a singular element of group $G$
with respect to the almost square root $A$.
All the other elements of group $G$ are represented uniquely as the product
of two elements of $A$.
If $Z(G)\neq\{e\}$ and $z\in Z(G)$, $z\neq e$,
then there are two possible cases, either $z=ab$, $a\neq b$ and $a,b\in A$ or
$z=a^2$ where $a\in A$.
In the first case
we have $z=ab=ba$ and $z^2=a^2b^2=b^2a^2$;
but this contradicts the uniqueness of the singular element
(if $a^2=b^2$, then $z^2=a^4$ and see the second case).
In the second case
we have $z=a^2$. Since the order of $G$ is odd, it follows that
$a\in Z(G)$ and $ab=ba$ for each $b\in A$. Hence $|A|=2$ and $|G|=3$.
This is a contradiction and the lemma is proved.
Lemma 2.
Let $G$ be a group of order $675=3^3\cdot5^2$.
Then $Z(G)\neq\{e\}$.
Proof.
Using the small groups library of GAP
we can prove of Lemma 2 by the following GAP
commands:
a:=AllSmallGroups(675);;
Filtered(a,x->Size(Center(x))=1);
However, the same can easily be proved without GAP.