..you don't think the people who made both the game, the creation kit, and the workshop ever considered this? For all we know, the whole thing could be automated wonderfully. We'll just have to wait and see.
Yes, it could be that the auto thing will work...but that is a BIG hope. When you are running a lot of mods (and among them big Overhauls) there is bound to be conflict.
It really doesn't feel right this auto-update feature. I have a brain, I know how to use it, stop thinking for me!
When a Mod makes an update it updates the Readme too, and they say if there is a new conflict, so you can opt not to choose the update or wait for a compatibility patch. But if that update is installed automatically...well it could seriously mess your game.
I just hope there will be a way to opt not to have the auto-update, or at least a way to revert to a previous version.