Had to dust off my account just to respond to this.
I really hope this is a temporary decision that is reverted before this release goes public or at the very least continues to use the current method (and not temporary as indicated) and the %appdata% is only used by whatever is making them to make this change. (seen several theories in this post)
%appdata% is already a cluster fudge of a folder in general and is already bloated beyond belief by many other games/apps that store tons of crap in it.
And while I am a technical person who can easily navigate through it, and follow previously provided instructions to maintain multiple mods setups for different versions by updating the configs, it is going to be significantly more of a hassle for the non-experienced folks trying to manage multiple mods/versions or even just install mods in the first place.
Please please please!! rethink this choice!