Really just the start of an answer.
In the case $d=1$ and $M=m\neq 0\in \mathbb Z$, the result is the group $\mathbb Z[\frac{1}{m}]$, the set of rationals of the form $n/m^k$ for some $n\in \mathbb Z$ and $k\in \mathbb N$.
Analogous with the case $d=1$, if $M$ is $1-1$, this is the set of vectors in $\mathbb Q^d$ which can be written in the form $M^{-n}g$ for some $n>0$ and $g\in G$. It is a subset of $(\mathbb Z[\frac{1}{\det M}])^d$. It seems to depend on the eigenvalues of $M$.
For example, a simple case of $M$ being diagonal with $M_{ii}=d_i$ would give the limit $\prod_i \mathbb Z[\frac{1}{d_i}]$. If $M$ is diagonalizable with integer eigenvalues $d_i$, is this still true? I think so. What if it is diagonalizable but with arbitrary complex eigenvalues? I have no idea.
What if $M$ is non-diagonalizable? Non-invertible?
For the specific $M$, we can see that $M^2-6M+6=0$, so $M^{-2}(M-1) = \frac{1}{6}I$. That means that if $(x,y)$ is in the limit, then $\frac{1}{6}(x,y)$ is in the limit, so the limit is all of $(\mathbb Z[\frac{1}{6}])^2$.
This will always be the case for $2\times 2$ matrices whose trace is a multiple of its determinant - then the limit is $(\mathbb Z[\frac{1}{\det M}])^2$.
The same is true for $d\times d$ matrices, $M$, if all the coefficients of the characteristic polynomial, $p(x)=\det (xI-M)$, other than the degree $d$ term, are divisible by $\det M$. You lighten this restriction: if all the coefficients are divisible by $r(\det M)$, where $r(n)$ is the product of the distinct prime factors of $n$, then the limit is $(\mathbb Z[\frac{1}{\det M}])^d$.