When the resolution is set to lower than matrix native the game starts windowed. I have to go to video settings and switch to something else and revert the changes so it would be fullscreen again. Not that much of a problem, but I have to do it every time the game the game launches. Maybe there is some workaround for this?

Hello,
I have the same experience, but why do you want to play below the native screen resolution ?
Try to reduce in video advanced the graphics preset, if you have a low framerate.