the mod path is supposed to go into the AppData folder. That's how it works. All copies install the game files into C:\Program Files\Stardock Games\Sins of a Solar Empire, with User data going into C:\Users\[username]\AppData(or Application Data)\Local\Ironclad Games\Sins of a Solar Empire.
That's just how the game works.
this is very true. I tried to change it but it would not let me.
you can thank microsoft, not ironclad or stardock, for this arrangement