

Install cnc_ddraw via protontrick to be able to use custom res
FPS 30, TDP 3
edit the ja2.ini file to set a custom resolution. Set SCREEN_RESOLUTION = 25, and CUSTOM_SCREEN_RESOLUTION_X = 1024 CUSTOM_SCREEN_RESOLUTION_Y = 640. Or use the 16:10 Aspect Ratio Calculator to find the one that you like.
I launched the game with mod 1.13. After editing the JA2.ini file, the game works without problems.
Ja2.ini edit
FPS 30, TDP 3
UI is small but manageable
At resolutions other than native, the game launches in the top right corner with large black spaces at the bottom and to the right.
In the JA2.ini file, set the resolution to 9 (1280x800) and PLAY_INTRO to 0. The latest 1.13 version of the mod can be downloaded here https://github.com/1dot13/source/releases
Game pretty much works as intended out of the box if playing vanilla. Played up to th assault on Drassen so far.

Working with proton 5.13-6
Graphics where very red in current proton versions, switching to 5.13-6 fixed that glitches.
Not all keyboard shortcuts seem to be working

Works out of the box.
I did not test any mods. Base game runs perfectly.