So when Janeway spoke to Picard in Nemesis, she was a holodeck character communicating with the real world from inside a program that was designed to pretend it was the real world?
Ah, but Picard in Nemesis wasn't in the real world anymore.
He was still in the Nexus, living out the "I'mma action movie hero now!" fantasies that he began by going 'back' to Veridian III to whup Soran's ass, and then going on to kick the Borg queen's ass, then kicking Ru'afo's ass, and finally ending with him kicking his own
ass by way of his mini-me, Shinzon.
(Talk about self-loathing. Talk about transference. Sigmund Freud would have a field day with all Picard's neuroses.)
Nexus!Janeway talking to Picard in Nemesis is actually a sub-reality existing within a sub-reality.
All the meanwhile, Starfleet mourned the loss of the entire Enterprise crew when the Veridian system went nova... but they quickly moved on to assigning NCC 1701-E to a brand new crew, who are still out there... somewhere... not that we've ever met them, or anything.