Are Peano's axioms number theory? No one really uses them directly (other than induction) when working on practical number theory problems, but they are considered part of it.

Scales and chords build the fundamental basic blocks for Western music (I would introduce equal temperament third but that's only a matter of ordering). They are taken for granted in musical practice, I agree, but only because musical practice concerns itself about how/what to play and why. If somebody comes from the point of view that clefs and stems (which are undoubtedly musical tools) are gatekeeping and all you need is a piano roll, this article explains from first principles enough musical building blocks to tell them why they're wrong.