I found that the display flashed a lot when the graphics setttings were on high. Reducing the settings (Quality and Anti Aliasing) to as low as available mostly solved the flashing. It was still quite annoying when displaying the map of the Greece coastline area.

After playing for a while, the game would show a black display, followed by a "Fatal Error" pop-up when transitioning from one area to another (e.g. from a cellar to the outside world). The "workaround" was to save the game and exit to desktop whenever a transition was about to be made. Often, restarting after such a save and exit would show the black screen followed by "Fatal error" pop-up. I feel it is highly likely that this is an issue with te game, rather than Proton.

On occasion, the "interaction" button stopped working (so "A" on my xbox controller clone). This is not a controller issue, the mapped keyboard key ('F' I think) did not work either, and all other motion and attack controls were working. "Fix" is to save and exit, and then restart. Seems like a game bug.