Well, waveform shapes are more about the instrument design itself, rather than harmony. A basic waveshape will always be harmonic and contain only harmonic partials. Of course if you manipulate the waveshape with things like FM, you will get more varied partials that are not necessarily in the harmonic series (they will sound more "metallic" instead of harmonic).

Music theory mostly deals with instruments that have harmonic series — or close enough to it (real world is never perfect), others are considered more like tuned percussion (i.e bells) or atonal (so used mostly for rhythm or background).

But you don't have to look at classical theory only. You know powerchords in metal are very popular and that's because most other chords sound pretty bad with a distorted sound like that from an amp. So it uses mostly octave and powerchords. This is not a "rule" like I said it's just experience or math that others simply don't sound as good. Theory does deal with certain quicks depending on instrument as above, but in most cases it is more generic.

Waveshapes like I said are more about sound design and instrument design, not music theory.

 

this is just the beginning. It get's tougher when it comes to scales and then chords. However, I'd recommend Skill Shares' Music Theory on Midi Grid. Very useful one! Learned a lot from it. Now, with every day passed I'm getting good at writing chords and Melodies myself, the problem is that I still can't recognize intervals by ear except for minor 2nd, major 2nd, minor 3rd, major 3rd, unison. I'm using ear trainer pro software to do this. I'd recommend it for you, if you want to learn intervals.