Your builder is right - they only offer heat coating with the black header pipe... But take a look at a bike with D&D's and see if you can see the header pipe with the heat shield on...
I'd see it, Scott. I don't see the forest. Only individual trees, saplings, blades of grass, pine needles, leaves, twigs, and sticks. I had LASIK eye surgery 6 years ago, and during that 30 minute procedure I went from 20/400 to 20/15. Though my night vision has eroded due to the surgery (tradeoff), and I'm starting to notice a decrease in sharpness, my eyes still pick up every little detail. I'd see it.

Unlike Chip, the reflection of the bluing in the side cover has never bothered me, but now that it's been brought to my attention, I'm lead to rethink my position on the installation of plain stock headers without jet coating.
Headed to Hanceville in the morning to gather options and see how much time this will add to the project.