Alright, I intended to reply to this post way earlier, since I thought I knew the cause, but I did even more digging and so... I present to you at least some sort of a solution...
First, the issue:
The issue is with DirectX9, or at least, that's the biggest suspect from what I've found. I tested four old games (Guild wars, Kao the kangaroo, Payday2 and Metin2) with a laptop that runs Ubuntu 20.04 with NVIDIA 3050 and AMD 5600H and launched all of the games with Proton 7.0. Only Metin 2 didn't work, but I think that's because it's a private server and launcher so... that may be its own can of worms. Other than that, no flickering with Guild Wars 2, no crashes, no issues whatsoever. All of the games mentioned above immediately crash on Windows 10 Desktop with Radeon 6800XT and AMD 3800X (except Guild Wars 2, I get the flickering too).
Now, why does it have to be DirectX9?
This is the best part. First of all, all the games I've mentioned run on DX9, so that's first thing I noticed (old games). But, at the beginning, I thought that something might've happened with the 6800XT and since I still have my old NVIDIA 1070 that I used before upgrading to 6800XT, I switched them and tried running the games on it and as you can guess, all of the games worked without issues, even without NVIDIA drivers...
So, I started digging a bit deeper and found posts like these:
The actual "solution":
You can read through the posts, maybe find some actual and better solution, but to sum it up, the drivers seem to be screwed up for who knows how long and I still wasn't able to fix it for myself, but maybe if you try using the Vulkan API it may fix it for you.
Hope someone at least finds this useful or picks up on this, since I doubt I will bother with this anymore. The only other solution I can think of is installing Ubuntu and use Proton as a fix (add a non steam game and force proton compatibility). However, I didn't test Ubuntu with an AMD GPU so, I don't know the results, I read that people tried it and said it worked for them, so... try your luck I guess.