I don't know about the billing, but I believe both are actually being used as backstops for non COVID patients. People are complaining that Mercy only has 20 patients on it so far...because they're getting tested before they can be admitted.
Which only makes sense.
Proper isolation for an infectious patient means a room that's "negative pressure." That means the ventilation system exhausts slightly more air than it supplies. The result is that when the door is opened, air moves from the corridor into the room rather than pushing potentially contaminated air out of the room into the corridor. City hospitals generally have at least some such rooms. A military hospital ship is probably more oriented toward treating physical injuries rather than infectious diseases. I doubt the ship has any negative pressure rooms or wards, and I doubt that a ship's ventilation system can be easily adjusted to create such.
I know a guy who is an IT manager for Yale-New Haven hospital in (naturally) New Haven. A few years ago Yale built a new building specifically for treating cancer patients, the Smilow Cancer Center. My friend told me that Yale has emptied the top three floors of Smilow and is converting them to treat only Covid-19 patients. Why? Because the rooms on those three floors are all negative pressure rooms.
Dealing with something like Covid-19 is the opposite of treating people with suppressed immune systems. In those cases, the goal in positive pressure rooms, to prevent bugs in the corridor from getting into the room when the door is opened.