Why does it matter which kun-yomi reading I use

Are you referring to the pink kanji reviews?
For those, the WK devs chose what they consider to be the “most useful” (most widely-applicable) reading for the kanji, so that if you encounter the kanji in a compound word you haven’t seen before, hopefully your first guess will be the correct reading. Most compound kanji words use on’yomi, so most of WK’s pink kanji reviews will ask you for on’yomi.

All that being said, which single reading is “most useful” is admittedly arbitrary, so if you input a correct reading that isn’t the one being asked for, you’re prompted for a retry instead of being marked wrong.

 

While we’re on the subject, I’d highly recommend that you install this userscript: [Userscript] WaniKani Katakana Madness
It’s a good way to passively keep straight which readings are on’yomi and which readings are kun’yomi, because the pink kanji reviews that want on’yomi will always display your answer in カタカナ.

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