having 2 people co-op together with exactly the same mods
would be a severe technical difficulty itself.
You can't be serious with this part. "Severe Technical difficulty"? What?
Does the list of loaded mods match?
If No: Prompt users that they have different mods, highlight the differences.
If Yes:
Does the checksum of each mod folder match that of the other?
If No: Promt users that they have different versions of mods, and that they need to resolve this issue or disable the mod.
If Yes:
Congrats, you are now clear to join Co-op Multiplayer with a real friend instead of some mindless NPC who stands in the doorway while you get the snot kicked out of you while trying to run away from a fight you can't win.
Do you have to change any content?
No! It will be up to the players to recognize that they are going to be able to face harder challenges together than they could alone with an NPC companion. They can up the difficulty slider, or impose house rules on themselves. Beyond the considerable, but not impossible, task of implementing basic two-player Co-op into the game, this requires no extra effort as far as game design goes.
The second player merely takes the place of the NPC companion. They don't need dialog of their own, they don't need interactions with the world, they are a companion to the main player. A side kick. A friend of the hero who is along for the journey and who has no more impact on the game world than the already existing NPC companions.
*Whine whine whine whine* "It TES is single player! Ignore the dozens of 'second players' already implemented for a stupid computer program to play" is a really stupid line to follow.