My understanding is that some techniques for using clear coat only will eventually result in rusty looking patches and kind of blotchiness than some people would find unappealing. As I recall, this is only an aesthetic problem.

I think it is only logical that if a pigmented paint prevents rust, then a chemically similar or identical method of applying a clearcoat would also prevent rust... perhaps clearcoat is designed to adhere to other paints and the pigmented paint is designed to adhere to the base material... and paint peeling off a clearcoat-only bike is harder to notice and touch-up.