The Magnus Archives theory I have that I think is the most true is: The reason Oliver dreamed of Gertrude at her desk instead in the tunnels is because her being at her desk is representative of how all the decisions she made as Archivist is really what ended up killing her.

What happened in the tunnels was due to Gertrude’s two biggest mistakes catching up to her. For one, she didn’t have anyone who could have helped her pull off her plan because all of her allies were dead or gone, mostly directly or indirectly by her hand. The other thing is that she had underestimated Elias for years despite knowing that he was Jonah Magnus. Both of these mistakes directly lead to her death, and both of these mistakes were made because she felt her role as an Archivist was to save the world above all else. Even if that meant using her friends as pawns or letting the Elias stuff go to focus on the rituals.

Gertrude died because she was The Archivist, and narratively I think that was the point Jon was supposed to take away from Oliver’s statement. That’s why her actual death and dream death doesn’t match up in a literal sense despite matching up in a symbolic sense.

(Also: Oliver’s dreams do tend to show the root cause of death instead the direct cause of death. In “Grifter’s Bone” he shows concern over a women’s ears, only for her later to die due to blunt force trauma that is driven by listening to a cursed band. So his dreams do seem to value overall cause instead of direct cause.)