Hello it is quite delayed but I found the solution to my problem.
I'll post it here now in case anybody has the same problem in the future.
Proton 5.0-9 didn't work for me however 4.11-13 did kind of work as I showed in the previous post. I (wrongly) assumed that the fact that most of the screen was black meant I couldn't click there. But it turns out you can, so the solution is to make a username and confirm it by clicking around in the black until you hit the confirm button. Then go to settings (by clicking around in the black) and change your primary adapter settings to any non windowed resolution (again by clicking around in the black) that will fix the visual glitch. From there you can actually set up the settings and resolution you want, which will carry over when you launch using the FAF client.
So @tatsu nothing is wrong with the tutorial, it seems maybe proton has some trouble with my unusual graphics card (quadro K1100M). You might however add some comment referring to this post in the description because I assume I won't be the only one who will experience this problem.
As for your previous troubleshooting questions:
- yes I do have a graphics driver this was not the issue (it is a good thing to check if you have the same problem though. I'm no linux expert but I used this stackexchange post to figure it out.
- Unplugging one screen made no difference.
- I followed your tutorial to the letter so naturally I had the launch options put in correctly already. One thing I found that is nice though is that you can setup steamplay to launch with a particular version of proton on the same screen. Just go to the bottom of the same tab that contain the launch options and set it to the protonversion that you want. That way I can still have the new proton 5.0-9 version as my default and only use 4.11-13 for FA. For anybody with the same problem you do have to change out the generated runfile when you switch protonversions. So if you follow this fix and launching from faf doesn't work anymore, that is because the runfile is still the 5.0-9 version while steam is setup for the 4.11-13 version.
One thing I wonder about but couldn't figure out is if you could force faf to launch full screen instead of windowed mode from the launch options. If this is possible all the clicking around in the dark could be circumvented.