I finished the game while having only two small issues:

1 Any regular controller/gamepad will cause the camera to spin around if connected.

2 The mouse movement is not very precise and at every click the cursor will move very slightly towards bottom right. This issue is fixed in recent Wine versions but not yet in Proton.

However the game can still be played in good conditions using only the keyboard (I rarely used the mouse). Alternatively it can be played with the Steam Controller set in WASD mode. Performance is good, without visual artifacts.