Kanji not presented in a logical order - how often does it happen?

as @Gorbit99 says, WK doesn’t rely on semantic-phonetic composition at all, that’s not how they teach kanji. However, there is a very cool user script that supplements WK lessons with that information and I highly recommend installing it:

I don’t think it would make much sense considering how many kanji can have the same reading due to semantic-composition. That’s simply not how WK is organized at all.