You have a good point about moisture. Ford coated the floors with a tar based stuff that cracks & traps moisture between it and the floor pan. Primers and paints were not something that Ford used on the floors much since their coating was supposed to do the job.
I have torn out interiors of many 51-57 Fords. All the floor pans were treated the same way. Primer, base enamel coat (same as base color of exterior of car), then poured in seam sealer at the seams and most of the floor recesses (to prevent floorcovering from sagging in to them). There was never any tar coating over the enamel paint. As I recall, most of them did have some type of tar-paper (similar to thin roofing felt under the jute backing and floor-covering, which was badly disintegrated by the time I got into it.
No matter which way you go; carpet or rubber mat, you are going to have water in contact with the metal. But carpet is like having nothing against water penetration.
After I had cut out and welded in all new floor panels, I sprayed the entire floor with acid etch, then I used a quality caulk for seam sealer. I primered the floor and sprayed two coats of base enamel. Next I cut out my own custom fit roofing felt, covering the floor completely and overlapping at seams. No jute, no sound deadener (as I feared these would hold moisture and create mold and cause rusting). But I suffered for it by having sizzling feet in the summertime.
That might have been reduced by keeping the muffler isolation panel under the floor, but it was not salvageable and I did not make a new one.
The other alternative would be to leave it in the garage when it's wet outside.
I have a one space garage and always keep one of the cars in there. The car I usually drive daily sits outside. Doesn't really matter. If you got the doors and windshield sealed good, you may not get leakage that way, but you will still drag rainwater, ice, snow, etc in onto the floor with your feet. I drive my cars daily, regardless of weather. That's what my car is for. This moisture thing is just something that you are never going to get perfect. You can reduce it and protect against it quite a bit though.