The apple pie tradition is actually descended from mince pie, a mainstay of early american cuisine consisting of minced meat and sometimes apples, alongside various spices. Not unlike a tourtierre. I'm guessing the cheese was more at home on the mince pie, but kept as a topping once apple pie took over.
Yeah cheese on apple pie is a thing, albeit an odd one. The fact that Lucas eats apple pie like that further solidifies in my head that one if not both of his parents must hail from the Midwest originally, which I’ve always assumed given the fact that Lucas has spent his whole life in Washington state but talks like a Midwesterner — you can really hear it when he says words like “bag” or “MAGA”, he says “beg” and “mega”. He also had a video at some point where he was mooing about people calling him names and he said not to “even call him Hoosier or dork” lol and I thought it was interesting that he would include Hoosier in that because 1) that’s not even really an insult, and 2) he doesn’t live somewhere where it would make sense to randomly call someone a Hoosier.