Greg Rucka, post-Infinite Crisis writer of the Supergirl series, was interviewed by CBR yesterday:
GR: ... A lot of what's happening in the very first, and even into the second, arc is that Kara is looking for her home - she's looking for the place that will be her home. And eventually, she will find - or make for herself - a home.
CBR: Nice. Is the Supergirl in your book and the Supergirl in the new "Supergirl and the Legion of Superheroes" (written by Mark Waid) the same Supergirl?
GR: (Laughs) I'm not touching that. I'm not giving that away. If Waid wants to give a definitive answer, he should absolutely feel free to - I'm not touching it. Part of the reason that we're doing this is for people to wonder about that and to figure out what the reconciliation is - if they are, in fact, the same.
You see, the problem is that I know what books are coming out prior to the questions you're asking, so I feel like, "I don't want to do it (reveal the answers) - it's good stuff! I don't want to give it away." It's not a clone, let's put it that way, all right? I will answer that the Legion Supergirl is not a clone of Kara - No clones. No cyborgs.
CBR: That's good to hear...
Mark Waid discussed Supergirl and the Legion this past weekend at WonderCon.