shoot. i hope Unchained doesn't have this issue. it's already been said that there will be no modding allowed.
I dont think it'll be the same issue as retail, since the private server went in and changed up the .pak file.
With the updated graphics (from what I understand they are being updated anyway)
it might change the file size of the .pak file and cause it to crash at random when retail updates, or not launch at all, not entirely sure if that'll be a problem or not. Though the mod itself might work without any problem out of the box as well.
Since there wont be any file difference from f2p and unchained, as far as I could tell from whats been said so far, modding it wont be much of an issue as we can test freely using the f2p version as they haven't ip blocked all the vpn's for testing purposes. (Highly unlikely they will, and assuming its an IP ban, could just be an account ban.) As long as someones willing to mess with it.
So I doubt we have much to worry about.
Edit:
Take this with a grain of salt, once the update hits we will know for sure.