Let me take you behind the curtain to when WaniKani was first made: Back then, I was making the content level by level, not able to think ahead too far. Although I was checking vocab lists and such, there were plenty of occasions where I picked kun’yomi for “the reading” and was okay with it. Then, 20 levels later, I realize (due to needing vocabulary for these later kanji) that maybe on’yomi may have been better. But, at that point there’s no way to change.
So, philosophy still applies (learn the most useful reading), but now we were able to make those decisions with a better view of everything.
That said, there are probably quite a few that are right on the line, at which point we still leaned on’yomi for consistency –– so for those, I’m sorry! 