Are you staying at the Hotel Nikko Kansai Airport? If so, then I don't really see a problem with the semi-interlining of baggage. However, my bigger question is "will they even accept your baggage?" since you won't be staying there (or will you be returning back to KIX the same day?). And if you're not staying there, I think you won't be able to do it since the airport is basically on an island and I can't think of any other hotels immediately in the vicinity.

And I wouldn't say 3 hours is "plenty" of time. You'd be surprised how long it can take to get through immigration, especially if there's only two people staffed. And on the way home, since you're meeting up with a friend, that should be no problem at all.