How many other mods have you installed? How many of them are in that location? I have installed several mods. Not one of them is in that location.
Of course, I have not installed BAT. I have installed BUG in "installed as a mod" mode and it is in the location I gave, not the My Documents location.
Also consider the single most popular mod: Fall From Heaven II. It also uses an installer. By default it installs into the location I gave. I expect just about everyone who has installed it, which is a lot of people, has it in that location. (It does also keep some data in My Documents, as do a few other mods, but not in that MODS folder.)
It is also possible that after Patch 3.19 there are no issue with the My Documents\...\MODS location. If so, it doesn't really matter which location you install them to, other than keeping things tidy. I prefer to keep all mods in the same place. (I have been known to examine the contents of a mod, as in "looking through the files", rather than just play them, so keeping them all together is good for that .)
You'd also have a problem if your computer was used by more than one person with each using a different user name (admittedly this is less common than it used to be). The BAT mod would be available to you but it would not be installed for anyone else since it is in your documents folder, but not theirs unless they do a complete addition install. Why install the same thing twice (or more)? In theory the correct setup would be that the BUG settings should be in your documents, but the mod itself should be with the program. That way everyone gets their own settings but shares the code and fixed data. That is the way the game itself is set up, with the user's settings in the user's folder (not all of which is in the documents folder, it keeps some stuff elsewhere) and everything else in the program's location.