Non-Linear storytelling has never been something that has bothered me. Basically the gist of is that Lord V has controlled and manipulated Clark's entire history in order for certain events to happen. He pretty much explained this, the Legion are even just realizing it themselves. Mxy it would seem has been prevented from his role as Clark's "guardian" or stopping Lord V and some kind of big civil war happened in the Fifth Dimension with Lord V gaining power and control .
Remember these are beings from a species who admire Superman ( and Batman in Batmite's case)...Lord V is tainting that or wants that admiration for himself. Morrison even has included the Legion, because as we know, their formation is directly influenced by their admiration for Superman and his legend. In my understanding of the uber-arc...Morrison is actually paying ultimate homage to Superman and just exactly what he means to everyone. I don't know if anyone else has picked up on that, but that is what I've taken from this.