Well yes but most citizens don't know about those, beyond a vague knowledge that there are enemies out there somewhere most of them don't know anything much about the wider galaxy and it's races. To the average shopkeeper or factory worker the reason Jekos has giant watery eyes that glow in the dark and are hurt by lights is because his mother badmouthed the local priest behind his back, and the noble's have twisted scions locked behind forbidden doors because they think themselves better than Him on Terra.
Abritrators probably know more than most, because it's partly their job to know more about the threats to the Imperium that can lurk within it, but I doubt many of them actually understand why mutants are mutants or the real significance of it. Priests would be similar, told to watch out for physical signs of spiritual corruption but not told why beyond some vague platitudes and sermons from higher ranking clergy.
I think the official treatment of mutants given in Dark Heresy was spiteful tolerance of the less mutated, they were used as slaves or low level menials by their communities and scape goats for whenever things went missing or anything else bad happened, but more mutated specimens were driven out to the edges of society or killed outright. Self sustaining populations were either enslaved as a group like on Tranch or periodically culled, or both.
It would actually be kinda neat to see a BL novel focused on non-Chaos aligned mutants living in the Imperium. A fall to darkness type story perhaps, with a minor mutant born to a poor family growing up mistreated and belittled even as he tries to be helpful until he runs away, falls in with a gang of underhive mutants, gradually becomes more embittered and evil and ultimately becomes a minor chaos champion during a rebellion as he embraces his mutant nature and gives into it.