But, Doctor Manhattan is only supposed to be effecting people who have been changed since Flashpoint. Saturn Girl wasn't changed by Flashpoint.
Also, they can't just say Dr. manhattan did ever stupid writing decision/mistake. I mean, they can, but eventually they'll just lose credability and look like idiots. Using him as a plot device/excuse to write a bunch of garbage and then blame it on him would basically ruin Rebirth. It makes a lot more sense that its a brand new Saturn Girl. Geoff Johns wrote the Rebirth special, and he definitely knows the Legion well enough to write them well, since he's the one that fixed them and their history with Superman in the first place. So, in my opinion the only explanation that makes sense is that its a rebooted Saturn Girl.
I still don't really trust DC, but I really don't think that Dr. Manhattan has any involvement with Saturn Girl. He's not just a plot device boogeyman that exists to screw up new things. He's already screwed things up, but he's not actively continuing to screw with things years after Flashpoint. That hooded guy (who isn't Manhattan) might mess with stuff, but he doesn't have mental powers and couldn't basically wipe the mind of Saturn Girl to the point where she'd act like the Rebirth version. So, the easiest explanation is that its a total reboot, with the second most likely being that Johns let a bit of his new 52 mediocrity come in to a generally great comic and just wrote a very, very bad version of Saturn Girl. I'll give him the benefit of the doubt that it was deliberate, since he's written the Legion stuck in the Present very well and knows that's not how the Saturn Girl he wrote before, or any of the other Legionaires, would act.
I mean, Johns is capable of writing complete garbage, especially in te New 52 (like his work with "Shazam" andthe Justice League), but until more evidence surfaces I'm saying its most likely a rebooted Legion, not Johns being terrible. That sucks because Legion doesn't need a reboot and I refuse to read any rebooted Legion stuff at this point, but it seems the most likely explanation to me