I don't know the exact limitations, but I am confident that ATR headers will help even a stock truck. When is it worth it is the key.
Josh Benedict ran the stock turbo with ATR headers at 16psi and hit 106 mph trap speeds. That's the best MPH for that boost level I've heard of on the stock turbo. Daron has hit that or a bit better at 20psi. Dig and others hit 108-110mph with the 20g.
I'm not saying it can't be done elsewhere, but Josh's truck did get some gains out of just the headers. He was waiting on the PTE turbo setup when he did the headers, and wanted to drive the truck, so he put the stocker turbo & dp on it.
I'm sure he can correct me if i had any errors...