I think the lore behind the codex, as well as Black Library's endorsement of authors, has been nothing but perfection since about the turn of the century. The universe has just expanded so much since Rogue Trader that the Imperium might as well be its own universe.
Horus Heresy is... Well, as you said, it's long. But it's incredibly tragic and allegorical to our own history - The Emperor simply wanted to unite Man for Man's sake, and it worked until his favored son, Horus discovered the corrupting power of power itself. In killing each other, Man perverted the Emperor's wishes - he became a God, not a father figure. For a story evolving from a tabletop game, it's incredibly complex and thought provoking.
If you're enjoying them, Dan Abnett (wrote the first HH book as well as a few more later on) also wrote the Gaunt's Ghosts series of novels - some of the best I've read, just as novels period, let alone as 40K books. I also immensely enjoyed the Chapter War/Soul Drinkers books, though they weren't terribly well written, they had strong narratives and the characters were second only to the Ghosts.
Then there's Ciaphas Cain, Eisenhorn, Ravenor... Yeah, there's a lot of Black Library books well worth looking into.
Lexicanum states that both of those Chapters were deleted from the list by the Emperor himself.
Given the state of affairs, it's not unreasonable to assume that given that the actual Astartes of the two chapters might have been assimilated into the Ultramarines/others, if they survived at all - that their Primarchs either fell even harder than Horus, or worse yet - encountered something that even the Emperor had not yet accounted for in his plan for humanity.
However, given that Leman Russ all but confirms that the Space Wolves have already killed their brothers before the Heresy... Perhaps they were just corrupted before Horus made the traitors a serious threat. Or, as I said before - maybe they were corrupted by something that wasn't Chaos.
Doesn't have to be worse than Chaos. Basically there's nothing worse than Chaos, except Necrons but they don't posses you. I think those 2 Chapters either tried to make their own empire without obeying the Emperor or they went mad and killed each other.
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