I would describe it this way - when you unpack the mod to game folder - nothing is overwritten initially, you still have the same game you had, only some additional folders. Then when you run the "backup" script, your existing and current doctrine and database folders (whatever game version you use currently! it doesn't matter) are backed up in separate folders. Now you are safe, you can return to it in any moment (only not while in the game of course).
From this moment you can enable the mod by "install" script, or disable it with "uninstall" script". The uninstall will just revert your game to the state you had in the moment of backup. Doesn't matter if it was 1.01 or 1.01 with speed-noise fix or even some other mod - whatever. Just the version you had in the moment of backup is stored and you can return to it in any moment by using "uninstall mod" script. It takes about two seconds and you only should exit the game to do this :-).
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