When has 40k not been mashed up with anything? XD
Anyway, I am not into 40k, so I would leave that crossover to others who have a much more refined understanding of the WH40K aesthetic.
If I had to pick a favourite, then it would probably be Darjeeling.
I had planned Pyrrha to be in Maple High, since there are no analogues to a Greek school in GuP, also to play with the common fan joke that she must be Canadian in spirt (with all the moments of her saying "Sorry!")
Coco was to be in Kebab High due to their fancy fashion sense and coffee. Velvet was to be Koala Forest Academy because g'day mate. Penny; I envisioned her to be in Kuromorinine, same as Weiss. The villains and the Malachite twins were not in serious consideration when I started this project, but if I had to put them somewhere, I'd lump most of them into Bellwall Academy.
I don't think I'll be going back to this series anytime soon due to more upcoming projects, but thanks for the questions and your interest anyways.