Are they conflating cultures though? I haven't seen any claim by SP that there's meant to be any link between Japanese and Ainu culture in this game. As long as they bear the differences in mind and treat Ainu culture with respect, it should be perfectly fine.
Hate that I'm defending The Best War Games of all companies, but at the time of the game's setting, Hokkaido (or rather, Ezo) was a completely different country, just like Ryukyu was before the Meiji period. Hokkaido is legally considered Japanese now, but that's a relatively recent turn of events.