A crossover does NOT automatically mean the Flash shares the same universe as Supergirl. First of all, Supergirl herself in the pilot says that Superman was the only Super-Hero. Second of all, had Barry existed as the Flash in her universe she would have known about it.
Thus, two separate universes. So this crossover will likely be the Flash coming into Supergirl's universe via a portal from his Universe.
With that said, I CAN'T WAIT for this episode! Man, am I stoked!
One thing I really hope we see: A RACE!
Didn't Rip hunter though allude to seeing BOTH supes and Bats death in future on Flash Earth though?
or does he cross between seperate earths himself?
And still waiting to see smallsville supes showing up!