I actually dont know if a Famicom cartdrige can access the FDS sound chip, very good question. Youll have to do some googling on that.
For the phase stuff, FamiTracker has a sweep effect that happens to (almost accidentally) triggers a phase reset. I know some people use it as such. For us we could add a "phase reset" track in the effect panel. Like a simple thing that you set to 1 to trigger a phase reset. Feels hacky tho.
http://famitracker.com/wiki/index.php?title=Effects_Hxy_and_Ixy
Oh boy, a pitch unit is very fuzzy. Its the same units that you use in the pitch envelopes. Basically its gonna look something like this (this is in hexadecimal, trackers loooove hexadecimal):
http://famitracker.com/wiki/index.php?title=2A03/MMC5/VRC6_square_frequency_regi...
It basically measures the length of 1 cycle of the waveform.
So higher pitches have tiny values, which low pitches have HUGE values. So a delta of +1 or -1 will be a lot more significant in high-pitches. FamiStudio does not try to compensate for any of this. You can probably hear it already on instrument with vibrato.
-Mat