Mark X11 windows as override-redirect.
Defined in SDL_hints.h
#define SDL_HINT_X11_FORCE_OVERRIDE_REDIRECT "SDL_X11_FORCE_OVERRIDE_REDIRECT"
If set, this might increase framerate at the expense of the desktop not working as expected. Override-redirect windows aren't noticed by the window manager at all.
You should probably only use this for fullscreen windows, and you probably shouldn't even use it for that. But it's here if you want to try!