This is one area that I think will be endlessly debated...
My take on it is this falls along the lines of both LotN and Gothik. When author's write for Black Library, it's not as though the great minds-that-be do not check it for accuracy. While there are some certain dramatic licenses taken... these are primarily to both keep the world "fresh" and the tales different, not as a "THIS IS THE WAY IT SHOULD BE DAMMIT!"
BL has also been quite adamant that the Imperium is a fething big place. Just because Imperial Guard do something in the Ultima Segmentum doesn't mean they act the same way, or are even structured the same way as someone in the Segmentum Solar.
The same goes for Chaos. The decision to fall is really something that each individual Legionnaire/traitor made on his own, despite any sort of pressures placed on him from the outside world/immaterium. Therefore, if these reasons are not satisfied or found to be false, it would make sense to turn your back on something that let you down, whether it be the Imperium or Ruinous Powers.
Wow, fucking tangent.
Anyways, think of the Codicies (is that even a word? Firefox says no...) as one aspect, the "by-the-book" side of the Imperium/lore. However, distinct differences exist because every single human being/Space Marine/Chaos Marine/Ork or whatever is not stamped out of the same mold. Each character, each segmentum, is shaped from experiences/historical necessity, and act accordingly.
But yeah... this started out as a coherent message and turned into a ramble. So if this shit doesn't make sense... yeah sorry.