Scuba compressor: same deal
The same problems occur for the SCUBA compressor, and the dinghy motor.
In protected waters, the compressor mounts on a cockpit bench, with a cover, and the dinghy motor hangs on the pushpit.
On a small boat, if taking heavy objects like that on a passage, I think they need to be stored as low in the boat as possible. Which means draining the fuel, drying the tank and carb, and lashing them down in the Q-berth or sail locker.
Another possibility: I have even less storage space than you, but my boat's cockpit is over-sized. On the project list is to deck-over the back of the footwell, aft of the rudder post, to make a vented flammables locker. It might hold some combination of propane, extra fuel, and small engines. But not all at once.