The game is working as expected ever since Proton GE 7-42 got released (back in December). Should work on any newer version as well.
The game is completely fuctional if you use the protontricks, from start to finish, i hope some developer read this and fix this error.
protontricks 658150 d3dcompiler_43 and d3dx9_43
The fullscreen is not completely full in KDE, not even the fullscreen option works.
Protontricks is COMPLETELY necessary to start a level, if you don't use it, be prepared to receive a Shader Error in all of your screen. Without it, it only be playable trough the menu screen.
Go into game options, Betas tab, select "prevamped". It's a much older version of the game that runs in an SD resolution and lacks several new features and bugfixes, but it doesn't have the fatal vertex shader error.

Vertex Shader Error
Same error as everyone else is having, which is odd when the prologue and main menu work fine. I dug up one old report of it working on Proton 3.7-8, but if there's any veracity to that it was likely an older version of the game.

Crashes when choosing to begin the game
It gives this error after trying to start:
___________________________________________
############################################################################################
FATAL ERROR in Vertex Shader compilation
ShaderName: shWater
memory:67:22: error: syntax error, unexpected NEW_IDENTIFIER
at gml_Object_oOverworldWaterSprite_Draw_0
############################################################################################
--------------------------------------------------------------------------------------------
stack frame is
gml_Object_oOverworldWaterSprite_Draw_0 (line -1)