Hickory: My point is that there is simply NO reason for the EE version to completely remove ALL mods and overrides. None. For example, you might have a simple override (or a whole bunch of them) that a patch will have zero compatibility issues with, like replacement NPC portraits, or simple user item creations (to name just two).
What you suggest would require them to test all mods to see if it causes any problems and then only remove the ones that would. That's insane. Doing what you suggest could certainly cause tons of problems. So you leave that simple user item creation in. Ok, that sounds harmless, unless, the patch adds in (for whatever reason) and item that maybe uses the same item number or some other characteristic that conflicts with it.
It is not the company's role to police what you have, or don't have, in your game, regardless of any patch. It is up to mod creators and the user to ensure compatibility, not the company. As you said, you can't expect the company to ensure compatibility, but at the same time you should not be forced to reinstall everything just because of a minor patch.
I agree for a minor patch, it doesn't make sense to remove everything, but they have not released any minor patches. 1.1, 1.2 and 1.3 have all been major patches. As you say its not the company's job to police what you have, but the problem becomes when some user then goes on message boards and rails on how the patch totally screwed their game, when in reality its a conflict with a mod. It creates bad publicity for the company at best and at worst they spend a bunch of time trying to fix something that isn't their fault in the first place.