I think the only "universal" part of music theory is the integer resonance stuff, "a perfect fifth is a 2:3 frequency ratio", because integer resonances do seem to have biological significance for us. The rest is culturally dependent: it's not describing some uniquely necessary mathematical object, but more like describing the spoken language of a certain region and time period. The best way to understand it is to play music from that period, notice some common "moves" (like the move from dominant to tonic), and realize "hey, music theory has a name for that".

You wouldn't use music theory to write music, same as you wouldn't use a grammar book to write a novel. You write music by intuiting the sequence of moves you want to make, guided by your ear and listening experience, and maybe even coming up with some new ones. Then if you're successful, theorists will make theories about it.