Right, this is a fair point – but I’d argue that typing kana in the meaning box is not really a harmful association, since they come in pairs and it’s an easily detectable goof (and Meaning vs. Reading is less emphasised than having both that and the kanji vs. vocab cues). Plus, WK isn’t testing for anything that would be compromised by that.
But if your brain internalises that reading the word wrong is that kind of goof, it’s probably harmful to learning in the long run. And, these threads come up pretty frequently because people aren’t totally sure about how Japanese words work, so I think wanting to maintain that distinction is better, even if the inconsistency introduced by marking it as wrong also confuses those people.