1: Xavier was in on it.
The major Bombshell of this series is that almost all of the X-Men's history was staged and that Xavier, Moira, and Magneto were working in a long con. (Though they had a falling out at somepoint, so not all of the antagonism was faked.)
That's the retcon.
2: Presumably Scott has both eyes for the same reason that everyone who died in the last fifteen or so years is alive again. With Wolverine, that kind of assumes that Logan remembers what the Afterlife is like after coming back. Nobody seems to remember what they experienced while dead except for the ones that didn't pass on.
3: Timeline's dont' cease to exist when someone dies. the Age of Apocalypse continued to exist even after Legion's accidental murder of his father in the past was undone.
Moira dying causes her to reset in a new timeline, but that doesn't mean that the old timeline stops going. The stuff with the phalanx follows logically from Life Six, and I figure they showed it because it's gonna be relevant in a future storyline--Hickman's set to be in charge for years to come, and if nothing else the establishment of different kinds of hiveminds foreshadowed how Xavier used a hivemind to keep in touch with the X-Men this week.