The subframe and suspension is made of heavy gage steel, it takes some time to really rust away. If it were me I would cover the top but still make sure it gets ventilation from underneath and can breathe. Shortly before you are ready to install it I would then clean it up and paint. If I recall correctly some of the products like POR work better when applied over rust, and don’t work as well over bare metal.
I recently had my subframe blasted and powder coated, it’s probably more durable than the original factory finish. I will add the finish is beautiful, but I will only take my car out on sunny days. There are lots of durable coating products out there, probably more durable than powder coating.