I also keep two different Demul folders, one for Arcades and one for Dreamcast because they work better with a few different settings between them. I definitely keep the gpuDX11.ini as read-only.
I even had to make some ini files read-only in the Demul folder so the module doesn’t mess up my settings. I know that the Demul module for Hyperspin is a bit weird because it changes options by itself. The latest version of Demul is from mid 2018 and so far i have no issues with it as far as compatibility is concerned. But in the case of Dreamcast/Naomi/Atomiswave, Demul is just better and i can’t replace it with Flycast yet, even though i want to.
I absolutely prefer RetroArch as well, it’s far more graceful than any standalone emulator when you are trying to create a big couch/living room setup with the likes of Hyperspin and Launchbox.