Anything other than Proton 6.0 (any version) will not fully fill the screen. Part of the bottom will be cut off.

You must go to full screen for your controller to be registered. Otherwise, there is no Steam Overlay when windowed. In the Game settings, uncheck the joystick checkbox. Gamepads interfere with the keyboard controls once the main menu boots up. Map your gamepad to the default keyboard controls via Steam's controller configuration. One of the community guides has the controls listed out. The game will then work flawlessly.