That's right, it was the first arc of Ellis's run. During 'Counter-X'.
It was actually a pretty good storyline, but Ellis took X-Man right out of contiuity and sent him into a completely different direction. Thus the Maddy retcon.
White Jean is a pretty could guesstimate i'm reckoning.
I think one of the important clues that we're missing is: Why does Danger know Emma's secret? Danger possessed no form of telepathy that we know of and she was created prior to Emma being an X-Man. So.. Unless Emma did something dodgy in the Danger Room at one point.. It leads me to believe that the 'whedon's trick' is in Emma's perspective, not the external, omnipotent.
(Yeah I suppose the Envelope could have been Bogan's poker invitation, but I wonder what Seagle originally intended. It seemed to me that it was a set up for epic and interesting possibilities, and the mysterious figure had interesting nuances)