Yeah, I remember people trying to claim that TES happens later in the Fallout Universe just because of the stupid Nirnroot, but there were too many plot holes with that theory.
However, you could say that TES is the Fallout universe at its very beginning, sort of like how Tolkien's Middle Earth was meant to be seen as our world at its very beginning, despite magic and immortality not being real to us.
I think the godhead being some vault dweller in an experiment that makes him live out multiple different lives makes more sense though. Because of this you could just say that Nirnroot is actually a plant that grew naturally in the Fallout universe pre and post-war, and the godhead is just mentally constructing a plant familiar to him during the simulation. It also explains why when people like Talos realize they're the godhead, they either zero sum or gain manipulation over reality. They've realized that it's all just a simulation up until they die, in which case the simulation erases the dwellers memory and makes them begin anew.