That's a great question. I know my painter did mine all bass-ackwards. He painted the rockers, valances, and hood all black, then installed the hood, masked off the rockers and the Tutone on the hood (which I actually had to do because he screwed up laying down the template), then shot the body color. I had to install the valances myself (which I was fine with, honestly).
The whole hood treatment went weird - after I fixed the TuTone stencil (he'd put it on too far to the passenger side), his body guy went in behind the stencil, striped the voids, pulled the stencil, and then masked off the black area before shooting the body color.
I would imagine the cars are shot body color first - all of the cars initially would be painted a solid color. Then the cars receiving the TuTone paint treatment would go to a different area to have the rockers & valances masked & painted - with the cars receiving the TuTone hood treatment done at the same time. I'm guessing the rocker molding or decals (Mach 1, Boss 351, hockey stripes etc.) were probably applied in that same process once the paint had dried. Then back onto the assembly line.
That's just my guess on how it's all done.