Looks like this can be fixed for Subnautica by setting PROTON_USE_WINED3D11=1.

Is there a way to set those values for individual games?

would be cool if they had game profiles but i dont think so. what you can do is delete the prefix of the game change the setting and run the game then change the setting back.

Assuming you're using the Steam client, right click on the game, go to Properties, click Set Launch Options and set it to

PROTON_USE_WINE3D11=1 %command%

Will that work when the environment is already created.

Taken from the README.md (emphasis mine):

The best way to set these environment overrides for all games is by renaming "user_settings.sample.py" to "user_settings.py" and modifying it appropriately. If you want to set different PROTON_ variables than the "user_settings.py" for a specific game, use the Set Launch Options under the games Properties. You can launch the game as you would with PROTON_VARIABLE=1 %command% (source).

Based on that, I would say yes.

that is non sequitur but I will try it in a bit.

when i use WINE_D3D i have bug #79 again (on houseflipper as well)
plus i still have missing textures.

Worked for me with

PROTON_USE_WINE3D11=1 %command%

With a fresh comapdata folder. Running on SteamOS. However, I don't seem to have a Moise lock, but that is another issue. To fix it, I opened a menu and click the mouse and it was fine temporarily.

Worked for me with

PROTON_USE_WINE3D11=1 %command%

With a fresh comapdata folder. Running on SteamOS. However, I don't seem to have a Moise lock, but that is another issue. To fix it, I opened a menu and click the mouse and it was fine temporarily.

still have missing texures

With the latest proton I did not add any game arguments. I would try clearing your compatdata folder for the appid and try again on the latest proton. On ym.sode though I am using an Nvidia card with the nvidia driver via SteamOS.