Finger positions are learnt through muscle memory, not reading the sheet, and isomorphic notation would not help for all instruments anyway. Guitar, mostly and that's why you have tabs. Trumpet, only for certain pairs of notes (G-C, C-F, F-Bb are played very differently). Saxophone, mostly no. Clarinet, hell no it's a mess of an instrument.
The problem is "a third apart" means different things depending on where on the diatonic scale that third is. What I actually care about is how many MIDI note numbers apart it is, because that's what corresponds to the finger positions on the instrument.
>G# and Ab aren't even played the same on some instruments
Seeing as we've freed up the sharp and flat symbols, we can repurpose them to mean adjustments by whichever comma is relevant.