Well in the first segment, Rios mentions an anomaly, and it's green. Maybe she came from that.
That would have been my assumption, too.
And it sounds like
Sirena going to Seven is part of the normal present, no time travel or other meddling. But then again, they've done massive misdirections before, when Isa Briones spent the run-up of season 1 only ever talking about playing Dahj and never Soji, so the twin reveal would be a surprise...
But yeah, my main assumption is that Seven taking over
La Sirena (at least for now) is meant to be the normal timeline and universe at the start of the season.
Though I do hope she didn't permanently deactivate the other holos. That would feel very out of character for someone who spent years being friends with
Voyager's EMH and thus knows that Emergency Holograms have a potential to become sentient when run a lot (which I would still argue seems to be the case for Rios's EH's). Seven's whole life story is gaining individuality and independence and self-determination - proving you are more than some centrally controlled artificial intelligence. In my opinion, she should have more respect for the holos than wiping them from the system because they "annoy her".
But we'll see if they'll actually elaborate on that, or if it was just something Jeri Ryan said.
(And if she means she deactivated them permanently, or they're just not around in that moment.)