I don't know what you mean with "incorrect layout blah blah" fix it yourself instead of removing the mod.
The mod fixes many things, and some of them are already listed on this wiki. It fixes even more though and that is a good thing. The mod really is essential because it removes effects which cannot otherwise be disabled and causes many people headaches.
> The game packages pre-existing mods
Yeah no sh!t sherlock. There is only one way to disable some effects, which means turning a 1 to a 0 inside some config files. Now riddle me this, which is more convinient: A) manually go into the game files and scroll through hundreds of files and lines to find the correct variable, or, B) drag and drop this mod into the gamefolder?
> There is no way to not include some changes from this mod
Yes there is. The changelog.txt file the mod comes with lists EXACTLY in which file to find every-single-change. So someone who really wants to change something is perfectly be able to. Did you even try the mod? Did you even spent ANY time looking at the mod or what is written on the mod page? I highly doubt it.