If I differentiate $$ Y = \pmatrix{a & b \\ c & d} \pmatrix {x \\ y} $$ with respect to the matrix on the left side, what do I get?
On one hand, I think I should get $\pmatrix{x \\ y}$ because it's a linear function.
On the other hand, I think I should get a 3-dimensional Jacobian matrix (if it's a real thing) where the each 4 entries are 2-d vectors
$$ {\partial Y \over \partial a} = \pmatrix{x \\ 0}, {\partial Y \over \partial b} = \pmatrix{y \\ 0} \\ {\partial Y \over \partial c} = \pmatrix{0 \\ x}, {\partial Y \over \partial d} = \pmatrix{0 \\ y} \\ $$
Which one is right?
You can look at your function as $Y : \Bbb{R}^4 \to \Bbb{R}^2$ given by $$Y(a,b,c,d) = \begin{pmatrix} a & b \\ c & d \end{pmatrix} \begin{pmatrix} x \\ y\end{pmatrix} = \begin{pmatrix} ax+by \\ cx+dy\end{pmatrix}$$
so clearly the second interpretation is correct. Te resulting $2\times 4$ matrix is $$\begin{pmatrix} \frac{\partial Y}{\partial a} & \frac{\partial Y}{\partial b} & \frac{\partial Y}{\partial c} & \frac{\partial Y}{\partial d} \end{pmatrix} = \begin{pmatrix} x & y & 0 & 0 \\ 0 & 0 & x & y\end{pmatrix}$$
as you calculated. Now, recall that the differential $DY(a,b,c, d)$ at a point $(a,b,c,d) \in \Bbb{R}^4$ is actually a linear map $\Bbb{R}^4\to\Bbb{R}^2$ whose matrix is precisely the above Jacobian.
Therefore it acts as
$$DY(a,b,c,d)\begin{pmatrix} a' \\ b' \\ c' \\ d'\end{pmatrix} = \begin{pmatrix} x & y & 0 & 0 \\ 0 & 0 & x & y\end{pmatrix}\begin{pmatrix} a' \\ b' \\ c' \\ d'\end{pmatrix} = \begin{pmatrix} a'x+b'y \\ c'x+d'y\end{pmatrix} = Y(a',b',c',d')$$
so the linear map $DY(a,b,c,d)$ is precisely $Y$ itself. This is because $Y$ is a linear map, as you noticed in your first interpretation.