I've seen SCR pipes wrapped, and the bracketry still in place. You'll have to use a smaller wrap. 1.5" instead of the more common 3". Which means more wrap to cover the same length of header. The heat shields cover the areas where the wrap goes around the brackets.
Also, I've had the pipes to my CX650 street scrambler wrapped for years. I use the siliver silicone header wrap sealant spray over them, and the last time I took the pipes off, I unwrapped them a little to make a small modification. The pipe under the wrap was just aluminized steel, and welded with a Flux-core welder, then painted with VHT header paint. Not one single spec of rust on those pipes. Not even the welds. And I live in NC, with humid summers that last forever, and I ride in the rain constantly.
Mostly for my case, the wrap is to keep the heat off my leg and to hide my welds. It works great for that. There's not a performance difference with or without. Or rather, if there is it's so negligible that my arse can't detect it.