While I haven’t listened to the podcast, this explanation has been mentioned elsewhere in these forums. When it comes to kun’yomi, a lot of the time I’ve encountered them somewhere, so they do seem common. Perhaps also since kun’yomi are used on their own it’s easier to pick up on, while on’yomi goes more unnoticed when they become parts of vocab. 
In any case, WK give you mnemonics for the on’yomi when they introduce the vocab that needs it. So, it’s not like they skip teaching you these readings.
But, if you wanna stay on top of things, I suggest just installing the Keisei-Semantic -Phonetic script as it lets you see the on’yomi reading(s) during lessons regardless of what is taught by WK + shows how it relates to other kanji with the same radicals.