OKAY, I understand! You do it that way.
They way I use SH3 Commander is only one install and browse to C:\Program Files\Ubisoft\GWX\ ... C:\Program Files\Ubisoft\NYG\ ... etc. etc.
As I said, it remembers the setting for (example) GWX ... if I want other settings for NYG it will have the same settings as for GWX.
Your solution is perfect.
However, did SH3 Commander not said: "you must install it in this directory C:\Program Files\SH3 Commander (otherwise it is incorrect)?
So you rename it to: C:\Program Files\SH3 Commander1 ??? etc. etc. without any problem?