At what point did Earth turn into a MiB-esque dumping ground for alien refugees?
At the point that they needed a new source of alien characters once Fort Rozz was out of the picture.
For most, if not all of last year I was under the impression that all the alien bad guys Kara was facing were escapees from that prison ship.
Well, with the exception of the White Martian. And J'onn.
Now, it seems there's a fairly large existing population of nonhumans living on Earth, to the point that there could be a fight club, underground bar (which seems to have transformed into an ABOVE ground bar in the past couple weeks),
We saw right at the start that the door was at ground level in an alley. It was "underground" in the metaphorical sense of something secretive and countercultural and/or extralegal.
The idea seems to be that the aliens were always here, but most of them stayed hidden until the amnesty act. It was just the criminals that came out in the open and made trouble, and that was mostly just the Ft. Rozz escapees. Contrary to hatemongering political rhetoric, most illegal immigrants are very law-abiding otherwise, precisely because they don't want to get discovered and deported.
There doesn't seem to be much in the way of regular transport from Earth to the rest of the universe, so all these people seem to just end up here to stay...
Well, that doesn't follow. If a lot of aliens are coming
to Earth, then there must be a fair amount of interstellar traffic in one direction, and it would logically have to go in the other direction too. I mean, it's not like they just fell out of the sky.
Remember in "Myriad" last season when Kelex casually mentioned that Superman was offworld? And the very next episode established that Kryptonians can't fly in space under their own power. So Superman must've had some way of traveling in space. Granted, he has a Legion flight ring, which would permit that, but it's also possible that he was, say, contacted by aliens who asked for his help and sent transportation for him.
Plus there are at least two White Martians and one Green Martian on Earth, probably more of the former. They have to have gotten here somehow.
Suddenly swapping the DEO cave for the much more exposed towers is one thing, but it seems that Supergirl's Earth has had a Flashpoint of its own that no one's noticed?
More just a retcon. I'm reminded of when
Angel was spun off of
Buffy the Vampire Slayer. In BtVS, the premise was that Sunnydale was full of monsters and demons because it sat on the Hellmouth. Implicitly, such things were less common elsewhere. But then Angel moved to Los Angeles for his spinoff, and it turned out the demonic community there was just as large.