So all done. Good news, my Iwata airbrush can push auto touchup paint and clear coat at 1:1 paint to thinner. Bad news, for some reason, when painting the roof (a horizontal surface) the color comes out a lighter blue. No idea why, I asked the company and they are contemplating it. It brushes on exactly right, and when I airbrushed a vertical surface it was pretty close. So it's not a thinner issue, or a metallic flake clog, etc.
Air brush common law says if your brush isn't clogging a larger nozzle doesn't matter, but I have the bigger nozzle coming from Amazon anyway so I can at least try lower pressure, higher volume. If I can get it the right color, I'll do it again. But meanwhile, my truck is de-rusted and watertight! It's a pretty innocuous spot on the roof that few people will ever notice, so not going to lose sleep over it. The California cost to have a body shop do the same would be about the same as the trade in value of my 17 year old truck.
If you have to remove the roof rack, here's what the middle pedestal looks like. This should tell you what you need to know! After removing the cross bars, and removing the three bolts at the front and rear ends of the roof rack, you a.) slide the rail backwards, then b.) turn it about 60 degrees out to get that oval shape out of a keyed hole in the rack. Not sure it's obvious otherwise.