If I'm not mistaken, the clones didn't have geostigma because they aren't real people. My understanding was that when Rufus called them spirits it was in a litteral sense. They're spirits formed from the Jenova cells absorbed into the Lifestream when Sephiroth was defeated. Because they weren't really anything more than fragments of Sephiroth they were able to join with Jenova to complete them and make them "normal." At least that's what I go out of it.