Whenever I have the mower deck exposed to work on something, I just hit it with whatever I have lying around, usually black Rustoleum. I don't care what it looks like, but I find it to be cheap insurance against deck corrosion. It also makes it easier to scrape the clumped grass off the underside of the deck.
My method has been to strip to bare metal, apply Por15 and once dry, spray a layer of the paint over it.
I don't expect the paint to be there forever but I feel like it's still not quite completing the job without it. If you look at a brand new mower in the showroom, it's going to be the same color underneath.