That’s exactly my thoughts on this matter. I made a on’yomi only userscript to have a way to only use onyomi, but maybe it would be better to learn it the way wanikani originally taught it - the most useful reading.
But あ is not the most useful reading of the kanji 明. So now I’m not sure if I should trust wanikani and learn their reading for the kanji cards or use the Wanikani Kanji Onyomi Only userscript to always learn the onyomi with the kanji.