There's always the option of having two entirely separate Windows installations. Might be overkill and a bit time consuming to set up, but it's simple and proven to work. Bonus, the games that require setup A to work won't even show up in setup B, and vice versa.

Windows has option for "hardware profiles" which may be able to help in this case.

@elszgensa

Whilst that would work it is a bit of a hassle to setup as you said.
A last resort if nothing else works.

@Tiido

I tried the options in device manager, but after switching to WDM drivers the changes carried over to both configurations.
Maybe I didn't do it right? How do hardware profiles work?

I don't actually know for sure if they are the solution, I messed with them briefly in past and I think I managed to make a similar setup work. It is possible the WDM driver purposefully tries to find and change conf of any existing VXD installation it is compatble with, so maybe now after you do VXD on one, things settle.