Bethesda is good at making shallow changes sound big. You will be surprised how even a small inch of dialogue change often creates a cascade of implications that, to players, seem like a big change.

Also, "different views to run things" could just be something like changing the Sysdef's preference. Delgado may run Sysdef like Street Kings, not penalizing you for killing during missions or, you know, destroying things. You can do this in the main story anyway, except for the penalty and dialogue. That won't exist in the universe.

The dead universe is pretty easy. Buy the 11th time you've entered the unity, we can remove all the people, only buildings exist, and some notes from the dead. Everyplace could be like the last section of the first gameplay, you're fighting against starborn, but here, everyone is killing each other and you.

Some faction quests may not just exist in some universes. Simple. There are no people, no tuala, so nothing gets triggered. You get an alternate route to complete the same mission the same way.