The short answer: no. Changing your exhaust won’t void your Ford warranty. In fact, warranties cannot legally be voided due to the addition of aftermarket parts.
That said, you might run into some coverage issues after updating your Ford. This is because any future problems with your exhaust system could potentially be blamed on the aftermarket parts rather than on Ford’s manufacturing plant. It will be more difficult to prove that certain repairs should be covered under warranty.
Since Ford’s warranty only covers issues caused by manufacturer defects or errors, you might miss out on some coverage by updating your Ford before your warranty period is up.