As far as I'm aware the heater core is original? the wet boots and stuff explains a bit but I'm more just curious how this happens.
Fe + O = Fe2O3

Just be lucky that's all it is, around here it would be rusted through. It doesn't even take moisture, over time the paint can get wore off under the carpet from stepping on it so many times and bare metal rusts, it's as simply as that. Unless you park it in an environment all the time with zero oxygen, it can happen, its just a matter of time, which our trucks have had a lot of.