Actually why doesn't Oxcom have this as standard to ease copying of the game for seperate mod folders.
It contradicts the recommended standard for Windows programs... Data/Config/Work directory is supposed to be in AppData (preferably) or My Documents, so that :
- different users of same computer can have separate savegames and preferences
- you can easily back up your data because it's all in the same place, and also uninstall the program while keeping your data for later
- protection against virus : for a users without admin rights, the entire Program Files tree is not writable. A malicious program may mess with your data, but at least it won't infect and alter the behaviour of other programs.
As you saw, the downside is that two copies of the same program will (try to) keep their files in the same place.