I believe those problems were rectified by the Dark Messiah team. Remember, it was built entirely on source, with inventories dialogue (I'm Australian) trees and a map if I am not mistaken.
Source engine is not able to handle enough big maps to have similar freedom feeling like in this game.
I don't need to see loading screens every time. I love Dark Messiah but it's another type of gameplay.
Really a strange idea to make a kind of Fallout in Source, regarding Cry Engine or Dunia engine possibilities...
I'm pretty satisfy with Fallout 3 in the actual engine. It's my point of view and modding will be easy even without a CS!