>>105916259
the zelda games infamously use flags in fucked up ways to control game progression/scene setup

they literally only stopped after Skyward Sword, in that you can do some shenanegains to put the game into a basically any plot/scene state you want by doing nonsense that results in you having control of link during attract mode (where the plot state and loaded scene are both turbo fucked up so they can do nicer camera pans with the weird mix of assets loaded). Twilight Princess has similar glitches. Wind Waker speedruns are built around it because the game is in one of a handful of major plot states and it very severely impacts map layouts and stuff, so going to places incompatible with the current state lets you get up to lots of goofy nonsense

ironically, OoT in all its fucked up glitchiness that's been found, doesn't use plot flags for very much other than saying "ok dont play this cutscene a second time"(and even then a lot of cutscene triggers ask about your inventory rather than the game/plot state) so there's not much you can do with them. i think the only current application is the flag for "player got caught by a gerudo once" gets cleared and recycled for something in the ganon tower collapse, i forget what but it does something very minor that ended up being important to a meme category like No Doors or something. most of the other "where are you in the plot" flags only influence stuff like weather effects

>>105916400
metroid prime did it. the color every boss flashes when hit is a base color modified just a teensy bit until the art team found it perfect, and some had to be changed in development as boss environments were changed slightly (lighting, fog, whatever; not technical changes just final art pass stuff)