It's the same with older games like Soldier of Fortune II where you can put on a 3rd party mod for sounds, weapons, etc. whether or not a patch is required. To restore the defaults the game has to be installed fresh again. Sometimes an update patch for pc games will need to see that as well.
Now for something X-Box 360 using more of a pc type interface the patches are optional updates similar to what is seen in the add/remove or Programs+Features where those can removed. Mods for pc games change the programming itself in games and often see new entries pointing at additional files added.