yes thats the point - it was the other way around; the rpgmaker menu was the one overriding the normal regular option. So I just reported it in case /created post for someone who might get this problem, so they can help themselves
This has affected the game for ages though and has been addressed.
Game Page:
FAQs about errors and suggested fixes.
Q: Game’s screen is stuck in 640x480 resolution? No sounds are playing? No BGM is playing? A: Please reset _ResetRMsetting.reg , then run the game again.
The RPGMaker fullscreen option in the F1 settings applies to ALL RPGM games [in this case specifically, all RPG Maker VX Ace games], not just the currently launched game. (Hence why the default F1 hotkey is blocked)