Yes, it's hard to learn the symbols that involve playing something (especially clefs and timing not being linear - see: https://www.youtube.com/watch?v=Eq3bUFgEcb4 for an amazing "documentary" on notation systems), but often finding the pitch/right note is the larger challenge (for beginners) than understanding the meaning of notes. Is this because we do not teach people to play songs with only one note, but many rhythms? I don't know.
But I do not think the point of affordances in notation is a great example, especially given all the alternatives (see the video above) which, although in some cases clearer (e.g. a instrument-morphic notation), struggle in other ways (too much space used, too unable to represent timing, not transferrable between instruments, etc).
The reality is also that our mind can adapt easily in such distinct systems as music notation to shifted realities. Sheet music for different instruments sometimes uses the same clefs, bars and all, but is several notes a part (eg... the music of Violin and Viola are notated differently, such that the notes of the respective instruments more or less span the whole bar without going too far above or below for the extreme notes of the instrument). Musicians usually have no trouble learning this abstract switch, even though the affordance, is just one symbol at the beginning of each bar - the groove of playing a different instrument adapts it. I know this does not seem the case for UI, which are perhaps just "too similar" to each other and merge and feel unnatural, or maybe the issue is that while using a new UI - like the github comment selector being expanded - other sites may keep the old UI and confuse our mental model of afforances - but for music, it's just not the problem I see modelled in the article...