Unless I'm mistaken, Famitracker's NSF output uses it's own engine. Which is fine if you just want to listen to an NSF file, but it is practically useless if you are looking to actually edit the music in game. Similarly, NSF to MIDI is a relatively easy conversion to make, but MIDI to NSF while preserving the original engine and music format is all but impossible.
NES music is challenging because there wasn't really a standard music format, and each game pretty much does its own thing as far as the way the music data is stored (though there's some overlap in some games --- for example Capcom used the same music driver for multiple games).
As far as I know there are not any general solutions to editing music in NES games. Common solutions either use game specific tools, or involve editing the score by hand.
... though I am currently working on a super secret project (general purpose music editor) which I'm hoping will address this, but it's a complicated project that I'm working on in my free time and I may or may not actually get around to finishing it, so I wouldn't hold my breath.