I mean, these color patches aren’t meant for the frontlit AGS-001. They’re meant for backlit devices like the AGS-101, DS Lite, IPS GBA mods, emulators, etc. If you’re playing a frontlit SP then just play the games without patches.
I get that, it's just, well, irksome. Maybe I'll see about getting one of those screen upgrade kits someday. It's more annoying for stuff like Blackthorne, where the color restoration is really dark for the 001 but without it the colors are downright fried. Thankfully that's not the case for FF5 though.
Again I do want to emphasize good work, even if this hack isn't quite for me.