Okay while bored on a routine drive to work I got to thinking about the consistent comment that Alpharius/Omegon are one soul in two bodies. This, in turn, brought up the point that a lot of the "chaos corruption" we see in the fluff/background talks about souls and deamons attacking souls and what not. Or even when it comes to prophecies and stuff (not just 40K in general) it is often talking about souls and all that.
Now combining all of this makes me wonder if there is a reason Alpharius (and Omegon) never really "fell" to chaos. Yes, they sided with Horus' rebellion (Cabal be damned), and yes others in the legion since have dabbled in the arcane arts. But we never really see any corruption or mutation or power enhancement from Alpharius. Is this because the gods couldn't affect him entirely because he only had half a soul.
We have - I think, although sources don't come to mind - seen that Alpharius and Omegon didn't always see eye-toe-eye perfectly, so while "one soul" they weren't "one mind". So maybe they couldn't be simultaneously controlled by influencing a single soul. The displacement of the soul parts meant no chaos entity could manipulate the whole?
Maybe it's also why they didn't seem to have a part to play in the "Great Game" or whatever because their fate was so convoluted with their separation of soul into twin bodies that their "role" could never be seen and it meant they didn't have one. They were rogue agents to the whims of the Gods and it offered them protection from manipulation?
I dunno, just random driving thoughts I guess.