Once again, the question of warranty is very subjective. I wouldn't think a header would cause your warranty to be voided unless it's proven to be the direct cause of the problem.
Sounds good in theory, in reality who really knows except the powers to be at almighty Ford.
The C.A.R.B. thing I believe pertains to smog or emissions requirements and has nothing to do with warranty validation.
You see what you want to see and you hear what you want to hear.........