Your poly-diffusion cap will be a MOSCAP. It may be the standard FET gate,
or it could be field ox. The threshold voltage of the latter can be expected to
vary a lot and its density will be low. Below, or near the VT you can expect a
series depletion capacitance to develop.
Poly depletion in POP caps can be a problem, the silicidation (if any) probably
does not extend to the bottom of the top plate since poly tends to be shot
fairly thick and if the poly is not extremely heavily doped then you can get some
depletion there too.
Depletion capacitance gives you a voltco and it will be nonlinear, causing
distortion / nonlinearity. Audio and RF guys won't be happy.