Lots of interesting theories..
Not sure about the OP's car but if your car leaks
you would get rust problems. The leak doesn't have to be into the cabin.. (wet carpets etc.) .. you could simply get water penetration into the sills from above.. (running down the pillars) or thrown up from the wheels.. or it could be a blocked drain (in the engine bay or from the sunroof).
That water could seep into closed sections or into the car, underneath the carpets (hence the little half-moon shaped drain holes at the rear of each footwell.. 156 had water ingress issues so it might explain why so many of those have rust. GTV is more hand-made, so more prospect of not all the metal being thoroughly sealed.
Any leak doesn't have to be major.. even a thimble full every winter will eventually eat its way out.
The rubber schutz coating doesn't help... but "thin" or no application of it isn't the problem. Water getting behing it, or being behind it is the problem. It will hold the water "helpfully" against the metal. The floor rusts because it's not galvanised. Check out the photos from the OP. The inner sill (galvanised) is immaculate.
Obviously the schutz can split and crack with age (the lip where the sill is welded to the floorpan allows the floor at the sill joint to corrode) but that's generally age-related.
The jacking points are battle-ship gauge steel and rarely start corrosion along the floor pan. The rust doesn't spread enough to lift the Schutz away from the floor (letting more moisture in).
I dunno how you would cure the issues.. If water is in the car, it has to come out.. but drain holes (the half-moon doodahs) can oftem be a weak spot (the draining water gets between the metal and the Scutz coating.