Pretty much the reason why brought back Kara. In fact, DC Comics has been running from this particular version of Supergirl for some time now, insisting that her backstory was too complex for casual readers.
The legend goes that shortly after taking over DC Comics, now-Co-Publisher Dan DiDio went to a Six Flags theme park where there were a number of DC Comics-themed attractions. At one of the rides, there were a number of characters' backstories presented, either on screens or printed on the walls, to keep people occupied in line. DiDio noted that the then-current Supergirl had an origin that he felt might confuse or alienate casual fans, and shortly thereafter got rid of the "Matrix" Supergirl and replaced her with a version who was, as the original had been, Superman's long-lost cousin from Krypton.