Ye olde Rogue Traders (the ones with the charters signed by The Emprah, or Primarchs), are pretty much above the Inquisition - which doesn't mean that the Inquisition won't try and fuck with them, but it means that they're likely to be more discrete about it, since they have no legal ground to stand on.
Chapter masters can fuck the Lex Imperia sideways, and nobody can do jack shit about it, unless the Inquisition gets annoyed - and again, even then, unless there's evidence of xeno or daemon taint, there's little they can legitimately do.
Chief Astropath, not Librarian.
Also, I thought Xenology had been established as non-canonical, not being a rulebook, and all.
Where have half-eldar been retconned? I don't recall seeing anything that says that they can't exist.
Wot? Source? My recollection is that there's something somewhere (I don't recall the source, so I'm not saying this is WoG, might have been from the rather non-fluffy Xenology) that suggests that the Eldar were actually engineered from proto-human stock - the same stock that later evolved on its own into modern humans, though not before the Deciever (or was it the Void Dragon?) managed to insert the Pariah gene. Thus humans are actually one of the few powerful species NOT created or uplifted by another race.