This is probably an edge/obscure case, but when running the Linux .sh executable in Steam Big Picture Mode/Steam Deck mode, the game window doesn't receive focus and won't recognize mouse clicks.  This prevents the onscreen menu from being accessed and thus the game can't be saved/loaded/etc.  Controller buttons are still recognized.  This might also affect other X11-based composite fullscreen setups.

Current workaround: Launch game in desktop mode.
Possible fixes: Godot-specific function to grab focus on launch OR allow keyboard/controller to open and control the in-game menu.