Unless something big has changed in the week I was gone for vacation mods are stored in AppData(At least on windows). My question is why, it kind of makes sense to put them there seeing as though AppData is always in the same place and PA is not always. However why not just store them in a folder called 'mods' in the PA directory. That way everything PA is in one place. This wouls solve the issue of Managing mods for different branches. Some mods break in PTE or in the stable branch. If mods were stored in per branch spaces(in the mods folder in the pa Dir) then then broken mods would not occur. I could be a total idiot and being missing something that is staring me in the face so feel free to tell me if I am.
PA is generally installed in Program Files, which requires Admin privileges to write to, meaning if/when mod management gets incorporated into the game itself, you'd need to run the game as Admin each time (and PAMM, too, which it used to need to). That is not a good thing, especially since mods can be pretty malicious if you want them to be.