These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Astelan presents an alternate interpretation of Lion El'Jonson in Angels of Darkness, that he was not the loyal son he appeared to be, and instead deliberately delayed his approach to Terra to see who would win the Horus Heresy, the Emperor or Horus. This was pretty firmly entrenched until the Horus Heresy started, where it shows that Jonson was fanatically loyal to the Emperor, believing that it was better the Space Marine Legions destroy each other than risk overthrowing the Emperor.
Cypher invokes this from one Segmentum to another. Is he the most vile and evil of the Fallen Angels, who is making his way to Terra in an attempt to kill the Emperor on the Golden Throne? Or is he the Fallen's only hope of redemption, instead trying to take the broken Lion Sword to the Emperor to be reforged and earn absolution in the Emperor's eyes? No one can seem to agree on it. Horus Heresy books show that he may have been the cause of Luther's fall to Chaos, while other books show him helping Imperial Guard troops defend themselves. Even Angels of Darkness is wary on the subject, indicating that he only wanted the gene-seed and didn't take part in tampering with the annihilus.