Some mods already do this so the settings don't conflict with each other. For some reason my gta_sa.set file is incompatible with MTA SA's and my resolution always gets reset. It's most likely to do with the widescreen fix, but that doesn't matter.
To those who don't understand. I want to have 2 separate User Files in Documents like
GTA San Andreas User Files
Multi Theft Auto User Files
to avoid conficts and because it's messy to have them both in same folder.