Think about numbers, it is not sorted phonetically, Even the alphabet is not. All those languages that use alphabet sort in exactly the same order regardless the pronunciation.

I don't think you're in a position to speak for all of humanity.

I meant a human as opposed to an algorithm.

Point being: kanji words aren't always sorted phonetically, for the reasons described in the article, so a user may not be surprised if they aren't. But when a human is sorting kanji words they do so phonetically by reading.