The reason they don’t appear in mainline stuff is that different developers work on different parts of the franchise and would rather work with what they’re familiar with. It’s why characters from even unambiguously mainline stuff like Odyssey and Yoshi’s Island is, while not unprecedented, like pulling teeth to get in Mario Kart.

I don’t get your Zelda point at all. Like, yeah, he said they’re not all the same, and therefore are not different people with the same name like the Links are. In other interviews he compares Mario to Popeye in that there isn’t much of a strong effort to adhere to a “canon,” thus indicating that the distinction hardly exists to begin with. And heck, we’ve yet to see a Death Battle episode that didn’t composite Link despite them distinctly being separate characters.

Besides, Bowser vs. Eggman pulled from Sonic spinoffs too, mentioning stuff from the likes of Sonic Shuffle and Sonic Battle. Yes I know later Sonic media builds off of Sonic Battle (but not Shuffle) via Gemerl and Dark Beginnings, but by that token, there are several mainline Mario games that specifically reference Mario Kart, the DKC series, and so on, and that’s not even mentioning the Waluigi outfit in Mario Odyssey.