Making it flat black will require a single stage paint to go on top of the clear instead of under it. This is a LOT more expensive due to the hours of labor added. They will have to mask off everything they don't want to paint, then use a block to sand only where the black paint will go. Plus, to make it so there is no major lip between the two layers of paint, they will probably airbrush it instead. That in itself is also very time consuming.
Sometimes they will put a satin finish over a 2 stage paint to get the same look, but that too is very expensive.
Not sure about the Rat Rod Black.