To make it even clearer which reading you’re answering with, you can use Katakana Madness Wanikani Katakana For Onyomi to make your pink kanji reviews display your on’yomi answers in カタカナ!
Despite there being thousands of kanji, there are only several hundred unique on’yomi readings, so there are tons of overlapping readings. But, if you have this script, it’s always super obvious which reading is which, and it even doubles as bonus exposure to katakana, which is something that I see many Japanese learners wish they had more of 