Earlier quoted context omitted.
The trouble with analysing "notes" in a composition (or even just with a polyphonic instrument) is the pesky harmonics. The timbre of different instruments produce harmonics that happen to be the fundamental frequencies of other notes.
Would it be possible to eke out the harmonics by saying (for 'x' type of guitar tuned in 'y' way with 'z' effect, harmonics look like this). Like if the fundamental frequency is f, then the whole note looks like 0db at f and -5db at 2 f and -10db at 3 f or something. Then, when you're looking at the frequency domain, you start from the lower notes and say "hmm, looks like there's a fundamental at f, are the expected…
By the way, the reason it is easier to use NNMF than try to implement your suggestion as a heuristic is because there's much more overlap between the different notes than you might think, and (worst of all) the timbre of the note:
1. evolves over time!
2. depends on the velocity of the note (how hard the string was strum)
3. and the notes actually interact with each other. If you play an E, the A string will mildly reverberate too because of the shared harmonics