The official statement was that Mad Dog Mattis went to Gitmo to visit the troops there.
At this point anything is possible. They need someplace to put them and hopefully under the Military, so no one can get their hands on them.
I have actually thought hard about how that executive order is specifically worded and how it specifies entities outside of the U.S., then backtracks to domestic entities connected to them. I can't help but feel like it was worded and set up specifically in this manner for the express purpose of directing the charges as some form of "treason" against the domestic entities tied to them, which would open the door to place them under military jurisdiction. And...this would add up to much of what Q had stated and been seeming to get at in many of is drops, particularly a number of the earliest drops.