In discussing this with Akura and the other Iseijin, the possibility was mentioned of making the undercover ID generic enough for such tasks. However, we felt that it would become too convoluted, and that it was best to just stick to KNF Trappers. If RP handwaving is needed, suppose that the Blood Dragons and Golden Chrysanthemums are close-knit enough that they would not be fooled when one of their own returned from Heaven's Gate. For one, they do have Ryuku in the system, and can probably track where their ships are. Infested Blood Dragons and Golden Chrysanthemums are still possible- they are just so deeply undercover that they act as completely ordinary members of those factions, including not docking on the Arch.
In other words, those pretending to be Dragons and GC will either go deep undercover (BD/GC IDs, including the repninja hostile to the Arch) or embrace their new destiny and become Hunters (Wild ID, ***DESTROY***).
EDIT: Or not change at all. Could do that too.
As for the repninja, I don't think it would be too difficult to make the Iseijin ID have the KNF ID repninja + proper Wild/Nomad rep.