I wonder....
Years ago, there was an arc in the Superman comics called New Krypton. In it, Superman was able to free the Bottle City of Kandor, which contained both Alura and Zor El, and the city eventually launched into space to become New Krypton. During that arc, Zor El was the benevolent scientist who became ambassador to Earth- who was then assassinated by Reactron in a plot cooked up by Sam Lane and a few others (not sure if Lex was involved here or not). This in turn led to hostilities, and eventually Earth launching Kryptonite nukes into space that destroyed New Krypton (because, really, the comics were not going to allow thousands of Kryptonians to remain alive).
Part of me feels that they could adapt this story for the show, with Argo City in the place of Kandor, putting Lex in the place of Sam Lane, and having Kara as the focal character instead of Clark. The only thing that brings me up short is that this would be something that should be a season-long story, so to cram it into, what, 15 episodes, or whatever they have left, really couldn't do it justice.
It's a general problem when DC started to generate up to billions of folks equal to Kal-el. He was supposed to be the Last Son. Having a cousin was ok. Then we got Daxamites and equally strong lots of Martians. Then Kryptonians by the 1000's pop up and sometimes genocidially killed.
IMHO, that was a mistake. They keep going back to Kal or Kara being something special, the greatest hero - when they are really not that hot. Kara gets knocked on her butt pretty easily by various aliens all the time.
That was one of the reasons we got the original Crisis on Infinite Earths, and why Supergirl was killed off it it- Editorial felt there were too many Kryptonians flying around (there was a Kryptonian HORSE for cryin' out loud), so they wanted them all killed off to leave only Superman.
At least with the Daxamites, they were highly xenophobic and preferred to stay in their home system and not interact with the galaxy at large, with Mon-El being the sole exception.
So the mid-series finale ended on a high note with a long awaited reunion. I would've liked to see more Kara, but Team Supergirl all got sufficient screen time, and those nightmare trips were crazy.
I'm sure they have, but maybe it was only in a group capacity.
Even if she isn't the final villain, it's possible her powers bring forth something cataclysmic.
Do we know where the boys were born?
I don't see how. Things happened differently in the Post-Crisis world. They likely won't get into specific changes unless it's part of the story, (or simply overlook things like the President saying Green Arrow was the first superhero even though Superman had been around) and unlike the DCU, there are only a handful of shows so I imagine each show can rewrite its own history without stepping on too many toes. (and all the main characters actually remember pre-Crisis thanks to J'onn, so it still "happened" in their memories)