I had an epiphany this morning...what if the Linda Danvers that Matrix merged with was the pre-Crisis Linda Danvers? Bear with me, and listen for a second.
In the 2nd volume of the pre-Crisis Supergirl title, issue 19, Supergirl's life and secret identity are taken over by her de-powered clone, comprised of the six small Supergirl clones from earlier in her crime-fighting career who had been exposed to gold kryptonite. When the clone remembers who she really is (she really thought she was Linda), Kara tells her that they'll find her a new identity.
Now, up until this point, the story on 'Post-Crisis' Earth was that the universe had been re-written, and everyone who was alive got a new history. This explained why certain characters (like Supergirl) disappeared with no memory. Since Linda Danvers was Supergirl's secret identity and couldn't exist without her, how did she get re-written into the fabric of the new universe? Answer: she is template-based on the clone Linda Danvers who was still kicking around the DC Universe under a different name.
The Supergirl clones were initially villains, and that would explain Linda's penchant for the occult and why she got lured in by the demon Buzz (perhaps some faded memory of Supergirl's short stint as Satan Girl). This Linda would also be a sort of lightning rod for Supergirl reality, which would account for the reason that the pre-Crisis version of Kara landed where Linda would find it, and why she was allowed to go in Kara's place to try and prevent the Crisis.
Further, when she arrived on Earth-1A, Superman scanned her with his microscopic vision. If she was something other than Kryptonian, he would have caught that immediately, as he did the wig and clothing material. She was also able to carry his child to term. You could argue that was because of Matrix's powers, but I maintain that Linda was still human in her physiology (or, as I just pointed out, likely inert Kryptonian).
What do you guys think? Linda Danvers is really the Super-Clones reborn, or I'm just crazy?