I don't think it matters at this abstraction layer? You reason about intervals, scales, chords etc the same regardless of the tuning system. That only matters f

I don't think it matters at this abstraction layer? You reason about intervals, scales, chords etc the same regardless of the tuning system. That only matters for sound production, which this doesn't do. It definitely assumes you're on a 12-tone system so is really only useful within western european music theory. But that is usually what people mean when they say "music theory" anyway.