You could prone someone anywhere, really. The beds on the various AF aeromed platforms are pretty tight, and designed to have someone strapped in pretty snugly, but there's no reason why you wouldn't be able to prone them if adequately sedated/paralyzed. Granted I've only flown on them once for a training mission, so I'm not intimately familiar with the different platforms. But my understanding is the C17 is the best aeromed platform as it's almost tailor built for aeromed missions. The others (KC135, C130, etc.) require some adaptations. All are capable of being pressurized as well, so really there's not a whole lot different in management of a critical care patient's ventilator on the ground vs in the air.
There used to be a few things they'd say, like to fill the ET tube baloon with saline instead of air due to the expansion at altitude. But I think they've moved away from this last I heard.
A big consideration, however, in management of COVID patients in the air is cabin airflow and avoiding contamination of everyone/everything. DoD just published some guidance on this. If you only have one bathroom on board, and a conscious patient, do you park them near the bathroom so they can go easily without spreading it around the cabin, but everyone has to walk past them, or do you part them far away, but then they move through the cabin and spread it as they go? When you need to eat/drink, if you're down an airstream from them when you take off PPE, you're exposing yourself. If at all possible you want to construct plastic barriers/curtains to control this. I know some platforms are capable of providing hookups to on board oxygen genators.
I don't know if I really answered your question or provided much insight, but if you have any more specific questions I can try to answer. I'm sure someone else here probably knows more than me and has more actual experience with stuff like this.
