I’ve got an 8BitDo controller and while individual application support varies in quality (had some weirdness with Dolphin not playing nice), Steam consistently recognizes it just fine, literally plug n play. Any standard remappings I would typically do through Steam.
I’d used mine for a few years without issue, but recently had a thing where the controller stopped talking to the dongle. The only way i could use it was if i plugged it in. That required a windows executable to fix unfortunately, but the dongle does work again now. And to your point, I needed windows to remap the paddles on the back, but not the standard buttons.
I recall running into this issue as well. Ended up just unplugging my keyboard before booting up the game lol.
My understanding is that it isn’t a linux problem, but a problem with Dark Souls 2 specifically. Like I’m pretty sure Windows users encounter this too.