They want to emphasize the memorization of one reading of a Kanji, to prepare for learning of vocabularies. Mnemonic / memorization done right, I may say.
Nonetheless, imo, even to remember On readings first, for items with multiple On readings, both On readings are not equal. Some are more important than others. Also, WaniKani sometimes doesn’t teach enough vocabularies to cover all major readings.
A while ago, I made a script to allow answering of multiple readings of a Kanji, including ones not being looked for (but one looked for has to be answered too). It may help reviewing Kanji after already knowing several related vocabularies.