The pronunciations of kanji correlate to different Chinese eras and areas.
The usage and choice of characters are influenced by Classical Chinese, which was the literary language in Japan until, uhm, recently-ish.
There is a very good recent YouTube video that explains the usage of Chinese characters in Japanese and which I recommend to anyone interested in the subject:
https://www.youtube.com/watch?v=CF3MRMBjd20
I was very impressed by the accuracy and knowledge displayed, as most of what is written and said on the subject is ehhh somewhat disappointing.