Fair enough on opening it up. As long as the Megamod lives forever, I'm happy.
Unclear on timeline for Lily's arrival. The vertibird had to have crashed in the 2240s since we meet its pilot in Novac in New Vegas. In the vanilla game I interpreted the crashed vertibird as being a sign that the Enclave were monitoring Arroyo nearby. You replaced the Mr. Handy with a wanamingo; were they trying to infest the Klamath sewers with them, in the same way that Redding's mines were? I guess that's unrelated to Lily.
The placement of the shack just north of Klamath also sort of confirms that people first settled the area a few years after Fallout 1. Lily could have been part of the Super Mutants marching northward (we learn about this in dialog from the Den) but chose to stick around to the Klamath area.
Because the vertibird crashed relatively recent to game start, I think putting Lily in Klamath is reasonable. She would have made the blade closer to F2 or FNV than F1.