I would not make this a standard windows tool, it would confuse the hell out of most comp users.
Note that command shells will tell you what the sym-link points to, in this example I used mklink /J to make the Rebellion's dev.exe mod directory the same as the normal game, from the DOS command prompt:-
C:> dir
Directory of C:\Users\NewHorizons\My Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion
12/01/2013 15:34 <DIR> .
12/01/2013 15:34 <DIR> ..
31/03/2012 07:14 <DIR> AutoRecord-SinglePlayer
... clipped ...
20/01/2013 11:22 <DIR> Debug
12/01/2013 18:44 <DIR> Mods-Rebellion v1.1
12/01/2013 15:34 <JUNCTION> Mods-Rebellion v1.1 Dev [C:\Users\NewHorizons\My Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Mods-Rebellion v1.1]
0 File(s) 0 bytes
21 Dir(s) 21,657,583,616 bytes free
The real name is shown in between [ and ].
or from Cygwin
$ ls -l
total 52
drwx------+ 1 NewHorizons None 0 Mar 31 2012 AutoRecord-SinglePlayer
... clipped ...
drwxr-xr-x+ 1 NewHorizons None 0 Jan 12 18:44 Mods-Rebellion v1.1
lrwxrwxrwx 1 NewHorizons None 111 Jan 12 15:34 Mods-Rebellion v1.1 Dev -> /cygdrive/c/Users/NewHorizons/My Documents/My Games/Ironclad Games/Sins of a Solar Empire Rebellion/Mods-Rebellion v1.1
Both show that the "Mods-Rebellion v1.1 Dev" directory is actually a sym-link to "Mods-Rebellion v1.1".
FWIW: Any Linux users should be fairly familiar with sym-links as Unix has had this feature for decades.