Avoiding the highly toxic sidetrack this topic has taken...
Shira CalpurniaI think it is more likely that GW didn't ask (demand?) them to include anything on the GK sorcery, which left FFG with the opportunity to ignore it. But again, that's just what I think, there's no way to know for sure.
That's probably it, yes. It may be as simple as depending on the individual editor who has oversight.
At other times, GW's IP guys intervene, either to direct the writers along a particular course, or to rule something out. The Dark Eldar, the Necrons, and the Grey Knights have all received treatment that brought newer material from the wargame into the RPG (it is no coincidence that the great heap of Dark Eldar material in Rogue Trader was written shortly after the new Dark Eldar codex came out). On the other side of things, details - sometimes large ones, sometimes tiny ones - have had to be changed on occasion because they venture into areas that GW didn't want FFG to go.
Regardless, everything gets checked over by GW. The same applies to the novels - even a brief glimpse of any of the authors' internet presence shows a collaborative approach. It doesn't necessarily hew to the idea of One True Canon, but common themes and elements are preserved, especially in the last seven or eight years.
FFG now finds itself in the very different role of catering to a bunch of fans who all have a different idea of how the setting "should" look like. It's pretty much a catch-22 because regardless of what they are going to write, the level of detail they strive to attain means that they will upset someone .
Case in point: In the first Only War beta, only the Triplex-pattern lasgun had a variable settings slider, which is actually in line with GW's original material (5E Guard Codex, Inquisitor rulebook) for once. However, a lot of fans, apparently utterly unaware of said material, lobbied for all lasguns getting this feature, because that's what it said in the Imperial Infantryman's Uplifting Primer - a Black Library book. And at some point, FFG caved in, someone said "feth this", and now any and all las weapons save cannons have it. In turn upsetting those who would rather stick with the original fluff, or who wanted more consistency between the different product lines (seeing as a charge slider was still described as a heretical modification in Black Crusade).
But this also illustrates the problems faced by games designers and writers (I distinguish the two because games design isn't entirely writing, and writing doesn't inherently include games design) working on established games and settings - both in terms of rules and background, there is a fine line to walk between breaking new ground, making something that works, and honouring what has come before. It's extremely difficult to navigate between "you changed it, now it's worse" and "you didn't change it enough, it's still awful", especially as every individual has their own sense of where those two points are (and how far apart they are). I tend to be fairly cautious when it comes to developing new background, even for my own use - I've always been careful to work from a foundation of existing material, and to make nods and gestures towards older stuff (I tried to work a Tonboyz reference into the Ork material in Edge of the Abyss - it wasn't allowed to stay)... but compared to some people I've encountered on the internet, I'm hideously progressive when it comes to incorporating new ideas and discarding old ones.