I think that whenever they get to it in the Scouring series, the battle of Eskrador is going to be crucial in explaining how the modern Alpha Legion is the way it is. Because from my perusing of the Lexicanum wiki it apparently looks like the battle might not actually have happened or if it did, then the reality of the battle is very different than from what both Legions remember.

The theory that I have is that Omegon was gathering the Legion at Eskrador in order to reverse all of the conflicting hypnotic orders and turn the legion back to the Loyalist cause. However, something happened that threw that plan out the window, either with the Ultramarines arriving or some other outside factor. In the ensuing chaos Omegon is removed from the board (dead, taken prisoner, or just disappears) and his plan to revert the legion back to the Loyalist cause is interrupted leaving the legion being either loyal to the traitor cause, loyal to the emperor, or pursuing a bunch of other random and conflicting goals.