Cowl.
Cowl is Peabody's handler, like it was Madrigal's handler.
So why was he interested in collecting copies of Die Lied der Erlking if he was in the same 'cell' of the Circle as Peabody and actively running him as an agent? Why not just ask him?
Just trying to deny the book to the other Heirs of Kemmler doesn't necessarily make sense, because his strategy was that it doesn't have to be him that summons the Hunt; he just wanted to highjack the ritual at the end.
As for whether the skinwalker Morgan lured into the atomic test was Shaggy, I have to agree that the fact it treated Morgan as essentially just a job to do rather than a personal vendetta suggests otherwise.
Six of them being locked up in the Well certainly weighs in favour of interpreting skinwalkers as among the beings who can reform after physical destruction, but it's possible previous Wardens who tangled with them simply found it easier to imprison them than put together sufficient energy to overwhelm their defenses by brute force. If the latter possibility is correct, that might actually be the difference between the "minimum security" central area and the peripheral tunnels.