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There are a lot of books on the subject, but the short answer is that it's just the most common standard at this point. Yes there are some things about it that don't make sense, but for whatever reason it seems to be the most coherent way for musicians to communicate using a common language.

It's popularity also has to do with what sounds pleasing to the ear (and brain) on a biological level.

A number of people have come up with alternative scales and notations systems over the years, but none of them have really stuck for one reason or another. Nonetheless, they are pretty fun to read about.

here's the whole history of notation https://en.wikipedia.org/wiki/Musical_notation

Also, if you aren't familiar with John Cage, you should check him out. His music and writing deals with a lot of the stuff you just brought up, and it's also a really great jumping off point to find other interesting artists and musicians.

Indeterminacy, a work he did with David Tudor is a great starting point https://www.youtube.com/watch?v=_lOMHUrgM_s