I would guess pinholes letting through the tiniest bit of contamination; could be ambient salt spray (e.g. sweaty dust, road dust, partially melted snow, etc.), condensation, just high humidity; and, if the paint is tight otherwise and the rust is black, it would seem to be Fe(II) i.e. a reducing atmosphere, oxygen-poor, so at least it's going slowly, and that means the paint is mostly doing its job except for where it's been compromised. Unfortunately I don't think there's much to do about that, other than grind it down and repaint it, and get it coated in enough layers to be sure it's not pinholed.
Possibly a microscope can confirm pinholing, but you'll have to inspect a lot of surface to tell, probably with a good scope, and... whatever. I suppose if you can do a fluorescent stain process that would be handy.
When done in use, keep it hosed down with fresh water, let it dry out, I suppose; keep it in a dry place, etc. About all you can do now is reduce continued growth.
Probably the engine, gearing or impeller(s) wears out before panels rust completely through anyway, and if not, patches are easy enough to weld in place (assuming you are so equipped, or can get someone to do it economically -- even a top professional should be able to do that for a couple hundred bucks, well under the thousand ish sale price of a new one?), then grind down and repaint.
Tim