Lynata said:
Let's keep in mind that, given how the 40k franchise is handled, one product does not necessarily have to "fit in" with another. I'm no expert on the novels in question, but I have heard enough of the Cain ones to realise that they feature a lot of contradictions with existing GW fluff.
Perhaps the best solution would be to houserule different versions of Commissars, depending on whether the group one is playing in prefers the GW-variant or a specific novel author's interpretation?
It's true that the Cain (and Gaunt) books feature contradictions with the general depiction of the Commissariat, but the point there is the contractions are intentional and acknowledged by both the characters in-universe and the authors out-universe.
And you can totally build something approaching a Cain or a Gaunt without houserules, it mostly resolves around focusing on different talents and purposefully not buying Summary Execution, among other things. It's just a matter of throwing enough XP at the PC, since Gaunt and Cain are clearly high-level characters in RPG terms. I actually drew up a just-for-fun Gaunt, and it's a matter of throwing talents like Master Orator and Into the Jaws of Hell in place of things like Intimidate +20. But ya, that's the bright side of the freeform advancement scheme OW offers.