The primarchs were genetically engineered and space marines are supposedly derived at least in part from their DNA. I don't think the imperium counts emperor-ordained modification as a mutation.

Or it's just overlooked because of their usefulness, like they do with the mechanicus and their worship of the omnissiah.

They're implanted with genetically-engineered organs, I'm not sure if they are themselves are genetically modified. I tend to think of them as augmented by biological implants, in the same way that members of the Mechanicus augment themselves with technological implants (as are the astartes, actually, in the case of the black carapace).

In any case, 'mutant' in 40k tends to mean a random deviation from the norm. There's 'abhumans' like ratlings and ogryns which are not random ('breed true') and astartes are more like them.