As a fellow learner, I'd say that there is no point. Languages are not logical — they grow organically. The Japanese borrowed a foreign writing system (from the Chinese) and used it to write Japanese. For words borrowed from Chinese, they used an approximation of the Chinese reading they were familiar with (whatever Chinese dialect was in relatively close contact with Japan and relatively high in prestige at the time). For native Japanese words, they used the Chinese character corresponding to the same (or a similar) idea, but kept the Japanese word. I haven’t studied Japanese in a million years, but if memory serves me, the more basic words tend to be original Japanese, while the more technical words tend to be borrowed from Chinese. It’s a difficult writing system, but it’s worked for hundreds of years.