As far as all of the obscure ones that I can think of off the top of my head:
-I have been into the Infused Grotto & Mount/Volcano where you find the head customization from killing the one enemy there and the weapon chest, in EB.
-I did get to the Avie's Camp in SC.
-I did go to the Hyperion Truth Network through a side quest in AN:BY and go to the house in AN:BL.
When you play with others, does your map still fill in so long as someone else visits these places and remain undiscovered for your game? That's the only thing I can think of at this point.