The elephant in the room regarding the podcast is that OF COURSE "it doesn't matter" as people have said here and there. Flooding the Nintendo tweets with K. Rool questions was mainly a fun distraction in the lead-up to E3, and one for which Nintendo came close to delivering a flawless non-answer.
They didn't, though, so there are kernels to dissect in my humble opinion.
They really shouldn't have chosen a "who's your favorite boss" question, or at least should have had answers prepared so they didn't have to pause for an awkward 10 seconds to search for an answer not named K. Rool. Granted, K. Rool legitimately might not have been any of their favorites, and they might not be nerds like us to the point of being able to recite the fine details of his classic fights. But that would've been THE point in the episode to make mention of K. Rool, given the large number of popular twitter responses inquiring about him (the one other question that got comparable prominence was "WHY DO WE HAVE TO PAY MORE FOR THE PORT?!?"). They made a conscious choice not to do so, in a way that wouldn't have necessarily been the case if it were just a few isolated, un-liked responses.
Which leads to my other point, Sam's throwaway line to the tune of "We have to show some love for the Kremlings, because they..." after which Todd interrupts, generically says "Yeah, they're great too," and they pretty quickly move on. Beyond the weirdness of her bringing up K. Rool's enemy race in a question about BOSSES, it's unusual that they didn't care to elaborate further. One could say they wanted to keep their focus on TF, or didn't know the character, but these were fans of Rare's games. The one who playtested DKC3 even spoke at length about how Kiddy Kong is his favorite.
Maybe it's conspiratorial to think a Kong who's almost certainly never coming back is kosher for discussion while a heavily-desired villain who realistically could return in a number of upcoming games isn't so much as namedropped. But maybe not. It certainly wouldn't take more than the Treehouse higher-ups giving them a quick heads-up to avoid mentioning K. Rool by name, with no further elaboration, if they thought that would give away an E3 surprise.
No real way to neatly tie that speculatory rambling with a bow. It was a fun mini-ride with this podcast, even if it yielded next to no information other than the TF port's "level skip" option.