There is a thread out on this from 2007 titled "Clear coating denim paint". You should be able to search and find it. From what i read on that thread it looks like there is a flat clear on the denim paint jobs.
Nothing in the process of painting a high gloss clear coat is any different than painting a low sheen or denim type of clear coat except for the chemical make up of the clear coat. The same methods are applied.
I was looking into this a bit myself. I found that after looking at a bunch of Harley color charts, that both the shiny and flat colors (in lots, but not necessarily all) use the same base coat. Then either a shiny or flat clear is applied.