Mine has done this since new with 4 miles on the odometer. I would not worry about it. Like in you're case, as soon as the engine is at normal operating temps the motor is silky smooth and quiet. I get 22 mpgs on the hwy with my 2wd, scab, 3:55 rear axle 5.0. And it's not burning any unusual amount of oil. I have also been using fully synthetic in my motor as of 1,000 miles on the truck since new. It's also my work truck and absolutely doesn't get babied, but I don't just start it up cold and drive off without a proper warm up either.

I've also researched the knock with the 5.0L motor since I was worried at first about it, but everything online points to a characteristic of the coyote motor, very common on the Mustang forums. In other words it should only be of concern if it continues the knock after the truck is fully warm, which neither you're truck or mine does.