Keep in mind Warhammer and Warhammer 40,000 are worlds where half truths, lies, propaganda, politics, legends and myths exist. The absolute truth which is implied when you talk about "canonical background" will never be known because of this. Everything we know about these worlds is from the viewpoints of people in them which are as a result incomplete and even sometimes incorrect. The truth is mutable, debatable and lost as the victors write the history...
Here's our standard line: Yes it's all official, but remember that we're reporting back from a time where stories aren't always true, or at least 100% accurate. If it has the 40K logo on it, it exists in the 40K universe. Or it was a legend that may well have happened. Or a rumour that may or may not have any truth behind it.
Let's put it another way: anything with a 40K logo on it is as official as any Codex... and at least as crammed full of rumours, distorted legends and half-truths.
I think the real problem for me, and I speak for no other, is that the topic as a "big question" doesn't matter. It's all as true as everything else, and all just as false/half-remembered/sort-of-true. The answer you are seeking is "Yes and no" or perhaps "Sometimes". And for me, that's the end of it.
Now, ask us some specifics, eg can Black Templars spit acid and we can answer that one, and many others. But again note that answer may well be "sometimes" or "it varies" or "depends".
But is it all true? Yes and no. Even though some of it is plainly contradictory? Yes and no. Do we deliberately contradict, retell with differences? Yes we do. Is the newer the stuff the truer it is? Yes and no. In some cases is it true that the older stuff is the truest? Yes and no. Maybe and sometimes. Depends and it varies.