As in this old answer, it's a special case when $\rm A$ has determinant $\rm\, \Delta = \pm1\ $ in the following
Theorem $\ $ If $\rm\,[x,y]\ \smash{\overset{A}\mapsto}\ [X,Y]\,$ is linear then $\: \rm\gcd(x,y)\mid \gcd(X,Y)\mid \Delta \gcd(x,y).\,$ Therefore $\rm \,\gcd(x,y) = \gcd(X,Y)\,$ if $\rm\,\gcd(X,Y)\,$ is coprime to $\Delta\,$ (e.g. if $\,\Delta = \pm1\,$ as in OP)
Proof $\ $ Inverting the linear map $\rm\,A\,$ by Cramer's Rule (i.e. scaling by the adjugate) yields
$$\rm \begin{eqnarray}
\rm a\ \color{#0a0}x\, +\, b\ \color{#0a0}y &=&\rm X\\[.4em]
\rm c\ \color{#0a0}x\, +\, d\ \color{#0a0}y &\ =\ &\rm Y\end{eqnarray}
\quad\Rightarrow\quad \begin{array}{} \rm\Delta\:\! x \ =\ \ \ \rm d\ \color{#c00}X\, -\, b\ \color{#c00}Y \\[.4em] \rm\Delta\:\! y\ =\ \rm {-}c\ \color{#c00}X\, +\, a\ \color{#c00}Y \end{array}\ ,\quad\ \Delta\ =\ ad-bc\qquad $$
Therefore, by $\rm\color{#c00}{RHS}$ system, $\rm\ n\ |\ \color{#c00}{X,Y}\ \Rightarrow\ n\ |\ \Delta\:\!x,\:\Delta\:\!y\ \Rightarrow\ n\ |\ gcd(\Delta\:\!x,\Delta\:\!y) = \Delta\gcd(x,y),\,$ by the gcd universal property and distributive law. $ $
In particular $\rm\ n = \gcd(X,Y) \mid \Delta\gcd(x,y).\ $
Further, $ $ by $\,\rm\color{#0a0}{LHS}\,$ system, $\rm\ n\mid \color{#0a0}{x,\,\,y}\ \Rightarrow\ n\mid X,Y\ \Rightarrow\ n\mid\gcd(X,Y)\,$ by gcd universal property.
In particular $\rm\ n = gcd(x,y)\mid \gcd(X,Y)$.
If $\rm\,\gcd(X,Y)\,$ is coprime to $\Delta$ then $\rm\,\gcd(X,Y)\mid \Delta \gcd(x,y)\Rightarrow \gcd(X,Y)\mid\gcd(x,y)\,$ by Euclid's Lemma, so the gcds are equal, by they divide each other (and $>0$ by convention) $\ $ QED
Remark $\ $ See here for many special-case applications. $ $ Below $\rm\,(m.n) :=\gcd(m,n)$.
$\rm \begin{eqnarray}
\rm {\bf Corollary}\quad a\ \color{0a0}x\, +\, b\ \color{0a0}y &=&\rm eX\\[.4em]
\rm c\ \color{0a0}x\, +\, d\ \color{0a0}y &\ =\ &\rm eY\end{eqnarray},\ \ (e,\Delta)\!=\!1\!=\!(X,Y)\,\Rightarrow\, (x,y) = e$
Proof $\rm\ \ (x,y)\mid eX,eY\Rightarrow (x,y)\mid (eX,eY) = e(X,Y) = e$.
By Theorem $\rm\ e^{\phantom {|^|}}\!\!\!\mid (ax\!+\!by,cx\!+\!dy)\mid \Delta(x,y)\Rightarrow e\mid(x,y)\,$ by $\,\rm (e,\Delta) = 1$.