I'm in agreement that any other Earths that remain are now undetectable to Earth Prime, and probably to each other as well.
In Supergirl, Brainy showed that there were no other alternates to be detected, but the fact that we had that short clip at the end of Crisis of other Earths proves that they are still there. They just can't see them anymore.
Think of it like a computer. If you delete something, you are not really deleting that item, you are just telling the computer to
erase the pathway to get to it. It is still retrievable, but not by most users. I think at some point they (being the CW heroes) will eventually rediscover how to contact them again, but for now they are considered 'gone.'
But, like with The Brainys, Beth, all the people from the bar on Supergirl, in the jumble of the recreation of the universe some 'glitches' happened. Bleed-over ocured and some people got displaced to Prime, and probably vice-versa as well. And they are stuck. With any remaining universes pretty much invisible to anyone on Earth Prime there is no place for them to go.
Which makes me wonder about all the people from the bar, like the (now) twin bartenders. Are they suffering the same thing that Beth/Alice is? Will they all?
Or, as Dr. says, are they just making this up on the fly merely for the sake of drama? I'm sure they could explain it away with some
techno-babble but I would like to have that explanation rather then leaving it as a mystery-event concerning just Beth and Alice.

OTOH, Lex told (evil) Winn Schott that he managed to get arrested within “16 hours” of arriving from “another Earth.” This implies a more recent - post-Crisis - event. Moreover, and unlike good Beth, Winn didn’t appear too surprised at the notion of multiple realities. And that, in turn, suggests that Winn used some sort of deliberate means (a wormhole gizmo?) to travel from his Earth-? to Earth-Prime.
Well they didn't say when Toyman was arrested, just that it happened 16 hours after arriving. Nail down that date and we'd know when he showed up on Earth Prime. And considering how long he has been aware of the transition before Lex met him he probably had plenty of time to get used to the idea. Plus, he loco!
Crisis erased the “rules.”
Great way to look at it!
Well, I wouldn't go that far.

The reason I cut some slack is because the Batsignal business was largely a background detail. And although some of the main characters took note of it, they didn’t - to their credit - fret over it. Indeed, just before she was ambushed, Kate was on her way to “suit up” to deal with the hostage situation. IOW, she didn’t care that she wasn’t “officially” signaled by GCPD. Duty called and Kate didn’t hesitate. Now, had Kate and co. gotten angst-y or preachy about the city’s apparent “rejection,”
that would have felt weird and forced.
It just seemed blatant in the way the very first question asked of the Commissioner is if the light was not on because Batwoman left the closet. For me, it was just an odd question to start with. But that could be because I would never consider even asking it!
On an aside, I just finished binging both seasons of Titans on DC Universe, and what a good show! (For the most part.) But what stood out was the Season 1 Finale where Dick returns to a Gotham being overcome with lawlessness. Compared to Batwoman's Gotham that is supposed to be in the same state, it shows that they really have a long way to go in order to depict the same thing as convincingly. It's like they left the 'Gotham in decline' part of the story behind...