This sounds related to the same issue that some people seem to have with Dark Souls: Prepare to Die edition. I've tested a little bit more, and some proton logs can be found below (the gist site doesn't seem to be allowing me to upload anything rn, so I've had to upload the logs to google drive).
From my testing, it seems the Dark Souls 3 controls are the same as the ones on Dark Souls Remastered, which does show the correct prompts. This leads me to believe the issue is, while related, not entirely the same as the one on DS1 Prepare to Die, since the controls on that one are half-keyboard half-controller and not at all what they say they are or should be. If you can get access to DS1 Remastered or someone who knows the controls for it, you should be able to use those for DS3 (edit: I'll give a basic run-down of the controls below).
I can also confirm that the issue persists on both Proton 3.16-9 (the default for DS3) and Proton 5.0-7 (the latest version at the time of posting).
One thought I had was that it could be less a Proton issue and more an issue with the port itself, in which case I don't know if it would be possible to fix it with anything short of modding - which obviously would be a pain. I'd need confirmation on that from someone with more expertise than me, though.
For now, the basic controls I found during testing were:
WASD to move, left click to use your right hand weapon, right-click to use your left hand weapon. Shift does a power attack or parries if you do it with your left hand. W+attack at the same time to kick, W+shift+attack at the same time to do a leaping attack. Although I didn't think to test it, try R for use item (which will do your healing), as that's what it is in DS Remastered. Pressing space will let you roll, holding it will let you run, and tapping it once you're running should make you jump.
I shared two screenshots of DS3 showing controller prompts when it shouldn't:
https://steamcommunity.com/sharedfiles/filedetails/?id=2092996790
https://steamcommunity.com/sharedfiles/filedetails/?id=2092997027
Link to both logs:
https://drive.google.com/drive/folders/1MFoiGQt_lutEZOJ6ZABTkJpUUtxT-6eV?usp=sharing
Also here's my system information (which I thankfully already had in a gist and so didn't need to upload to any external sites).
So I've done some further research, and I'm fairly sure it's an issue with them just not including a new graphic when they ported to PC. People experience this on windows as well, and nothing short of mods seems to fix it for DS1, 2 or 3. It seems only DS1 Remastered actually has built-in keyboard and mouse prompts. I would say to be cautious with using mods though, as some of the DS ports have anti-cheat software for online play that may detect the mods and get you in trouble, so try to play offline if you do use any. And of course, as I said before, the actual controls are still mapped to the keyboard, they just don't show on the prompts.
As far as Proton goes, I'm fairly certain this isn't related, but it would probably be better for someone with actual expertise to look into it on a more technical level.
proton 3.16-9x1 2020-05proton 5.0-7x1 2020-05
Darksouls 3 opens well enough, no lag that i'm seeing, but the prompts are controller ones, even at tutorial. no controller has ever been in with that game launched. healing, even jumping can't be done cause no control stick to press down, nor can heal during a boss battle