I have learned from your example: interestingly, it is altering the idea of fx processing per grain. At least in my interpretation of your description we have now a pre-granulation fx processing (or post fx granulation) – where the fx params are not changed per grain, although this would be possible too (e.g. the env could trigger positions).
Post granulation FFT processing per grain (I have done this once in the kitchen studies project) would lead to different results especially with short grains, that produce strong amplitude modulation, which means a difference in the spectrum.