D what is it that 1000's were dipped in from factory? That stuff has done a good job of keeping many 1000's relatively rust free.
There is nothing wrong with using good old deoxidene on surface rust. I would have no worries using it on the boot lid below. Deoxidene and scotchbrite or steelwool and scrub it. It will go black but you can keep scrubbing or wipe it off and then keep scrubbing till clean metal. Then wash it off with water. Then wipe the surface over with thinners or prepwash, then go about your normal repairs.
Deoxidene wont fix rust, it will only remove surface rust.
No need to scare monger about using it the way its intended.