Thanks for the suggestion :)
Windowed mode seems to have it issues as well. In makes a fullscreen sized window, with the game rendered in the lower left corner, the rest being black. In this case the mouse is also offset as to where it actually should be, making menu navigation almost impossible.
When i move it over to the main monitor and fullscreen the game again it does stay on that monitor, though it goes back to the secondary if i restart the game. Also when the game is fullscreened, i have the menu bars from my desktop overlapping, cutting off a chunk of my game.
I really hope this can be fixed, its a fun game.

I tried your suggestions, i tried 1024x786 windowed, i still made a fullsized window.
Alt+Enter sadly didnt get me any response, neither did Alt+F10 which usually works for maximized windows.
Also found out that if i pressed revert to the confirmation dialog when switching to windowed mode, caused the game to back to fullscreen, as expected, however it then went black, caught pretty much all inputs and locked my system. I ended up having to switch to a terminal to kill the process.
Im afraid there might be a lot of bugs in the linux build when it comes to mysetup atleast.

Yup. 2021 and still there.

It can work if you select after starting "windowed" confirm, change back to fullscreen and select the right resolution for full screen.
If you move your mouse out of the window it can mess it up again.
For windowed mode there is no resolution available matching the display well.
Should have kept my CRT setup I played it with back in the days