I don’t mean to parse your words, so I apologize in advance, but I don’t think of AF1 as being a civilian aircraft.
I also didn’t think the sub was necessarily manned. I admit that what I know about submarines will fit on a post-it note, but do they need to be submerged and moving to fire a missile? My impression was no and no, so why would there need to be a crew at all?
My ignorance probably has me off on the wrong track here and I don’t mind being corrected.