Considering Fallout 3's dungeons were pretty nonlinear (and made by the same level designers as Skyrim and presumably Fallout 4), I'd say it's a safe bet that their MO between the two franchises is different.
I'd also say that, despite their linearity, Skyrim's dungeons were a vast improvement over the copy-pasted crap in Oblivion. Oblivion's dungeons might be nonlinear, but the fact that they all look the same and have virtually no environmental storytelling going on (or any explanation as to why they're full of Minotaurs or Spriggans or Imps or whatever) made them a drag to explore. Skyrim has way more different types of dungeons, and they got way more creative with how they clutter rooms and what kind of lighting effects they add.
And most of Morrowind's dungeons were just tiny, probably as a response to criticism about Daggerfall's oversized and labyrinthine dungeons. Which all felt the same. (holy crap, I just realized. Oblivion's dungeons are basically just Daggerfall-Lite)