Other than the extremely avante garde New Music and some traditional micro tonal music (Indian Classical comes to mind), I'm not sure why you think this doesn't work for almost all music from ~1400 to the present day.

Even early choral scores, (~1200-1600) can be typeset by LilyPond using SMuFL compatible fonts in their traditional styles. (For examples, see the "Ancient Music" section of the documentation http://lilypond.org/doc/v2.18/Documentation/notation/ancient...)

Prior to that, there's not much written music, and that which is written is done so in a form so specific or esoteric that it will needs to be re-engraved into the traditional staff form for performance by modern day musicians.

There are some local variations that SMuFL doesn't really "handle" per-say, take Jianpu notation as one example. (https://en.wikipedia.org/wiki/Numbered_musical_notation) but those forms can typically be handled well by a standard text editing program.