I don't know of any supporting evidence, but it's possible some of these Chapters are operating under a polite fiction. These Chapters could be from Traitor Legions, but proved themselves loyal beyond a doubt. The powers that be pretend the Primarchs are unknown to keep these Chapters, instead of purging them.
There is also a chance that a Geneseed pool can mutate enough (possibly even intentionally) to not be clearly tied to a Primarch, without being so mutated as to fail the genetic testing.
Both options are speculation on my part.