I think Fourier-Mukai transform is related to the Fourier transforms you described through the space A \times \check A
which is symplectic and somehow relevant, though I don't know the details.
The reasoning is that when x, y, ...
live in A
, the vector fields kind of live in \check A
, so that's analogous to tehthe space C[x, y, ..., d/dx, d/dy, ...]
you mentioned above.