Well, that's sort of the point. With Frobisher, they aren't completely untrue. There is genetic engineering that has adapted humans to life on other planets.
Lets say that since the Star League era there have been rumors about genetically modified humans (which are somewhat true).
Then the Clans come back, having used genetic engineering to create the phenotypes, especially the Elemental and Aerospace phenotype.
And then someone with a conspiracy bent combines the Frobisher rumors with the Clan genetics. "Man, if the Clans have done THAT (Elemental and aerospace phenotypes) what ELSE might they have done? Monsters man, monsters!"
And then someone comes around and points out that if the Clans had been tinkering even further, that we'd see some evidence of it.
So conspiracy guy says "Man, that's right! So they're either hidden at the Homeworld slaving away on the half inhabitable planets (disproved by SERPENT), or maybe they're part of the Dark Caste!"
And from that conspiracy, you get the Genecaste, a heavily genetically modified Dark Caste that's running from the Clans.
And then since there's always been rumors about the Magistracy and Mermaids and Centaurs and what not, then the Genecaste gets linked to the Magistracy. And since one of the biggest unknowns in the Magistracy is the EM, that gets linked as well. And so you get the entire Genecaste conspiracy.
But..at the heart of it all, is the small kernel of truth that most conspiracy theories are built on, and that's the genetic modification of the people of Frobisher.