No, no, you've got it all wrong. Allow me to clarify, please, before anyone gets any more confused.
First there was Girlfriend of Steel (official English name: Iron Maiden), the Eva dating-sim-or-close-to-it that was supposed to take place at some point in the series. A little side story to give Shinji a romantic subplot, since the series is so utterly lacking in teen romance. The game was NOT based on the alternate reality of Episode 26.
The manga scanlations you've found are from the new Evangelion manga, Girlfriend of Steel
2, based off the game they'll be releasing in Japan shortly of the same name, which IS based off the alternate reality scene in Episode 26 (except that Kaoru is apparently in this version of events (yay! (no, I'm not gay, and neither is Kaoru, though I have my doubts about Shinji sometimes)), as is clear from the scanlations).
From what I've seen of the new manga (which is only the first chapter because that's all they have scanslated yet), I think it shows promise (even though the artist isn't Sadamoto). The first chapter ends with a nice twist that promises plenty of interesting things to come. And of all the characters introduced so far, only Misato, Ritsuko, and Kaoru seem to know what's going on.
Here's a very scary screenshot from the new game:
Why is it scary? Well... who does that look like in the yellow #4 plugsuit? And would you trust HIM with an Eva?
More at:
http://www.evangelion.ca/gamgirl22.html