This is what I have seen as well.
Decks normally rust out from clippings and water that collect on the top of the deck.
The bottom side of the deck is polished while mowing. You might be able to spray a rust inhibitor on the bottom side during the off season to keep the surface rust at bay, but no coating on earth will survive that environment.
If I were going through all of the trouble of removing the deck, I would have it bead blasted. A paint job is only as good as the prep work, and that's the cleanest slate to start with.