At special request, to help add flavour to the story, [url=http://warhammer40k.wikia.com/wiki/Space_Marines#Implantation_of_Astartes_Organs]here's a link going over all the gene-seed organs implanted into a Space Marine, and what those organs do.[/url] For sake of ease, one can assume that the Primarchs were born with and therefore possess most or all of these organs, where appropriate; for instance, they're unlikely to possess Progenoid Glands, since their gene-seed stock was already utilised to create their Legions in the first place, though their Marines would obviously possess them to allow the Legion to keep growing. If you want to have some of your Primarch's Astartes Organs be atrophied or mutated in some way to add flavour to both them and their Legion, I won't stop you, but just be aware that certain organs are absolutely vital for a Legion to function, namely the Progenoids and the Black Carapace, and others such as the Ossmodula and Biscopea are required to, e.g., allow the bearer to develop into Space Marines in the first place.