I'm not sure if or when Ford Performance will adapt there own exhaust system but just wanted to let you know that the Borla system does not void your factory warranty. Below is a expert from their FAQ section as well as a direct link to it.
BORLA FAQ LINK
Q. Will it void my factory warranty?
All Borla street Cat-Back™s, Rear Sections, and Mufflers are 50-state emissions legal. These systems will NOT void your factory warranty, some cars even have Borla systems as the OEM exhaust. In fact, it is illegal for a dealer to deny you the OE warranty because you have changed the exhaust system.
If your vehicle manufacturer fails to honor emission/warranty claims, contact EPA at (202) 260-2080 or
www.epa.gov. If federal warranty protection is denied, contact the FTC at (202) 326-3128 or
www.ftc.gov.
Not sure if any of that helps, just wanted to share b/c I had the same concerns prior to purchasing my exhaust.