Very frustrating— I have the same issue. I've taken it to two different dealerships a total of 3 times. First time, I was told there was nothing wrong, and when I insisted they take a closer look, they found the right rear break pad hadn't been fully seated at the factory and "fixed it". For the next three days, it worked flawlessly, blissfully silent brakes. Then over the that weekend they started quietly squeaking, only at low speeds. The following week they were full volume squealing like an old rusted school bus. I took it back to the dealer (same I bought from) and they looked it over again and said there's nothing wrong, the brakes are in great shape — good job me for not slamming the breaks by the way (6000 miles) — and they can't replicate the sound. I took the truck out into the parking lot and recorded the sound, then brought it back and played them the videos on my phone. Then the senior guy pulled me aside and said look, it's an issue people see on F-150s and Expeditions. Basically there's nothing wrong safety-wise, it just makes noise. If we switch out for softer pads or harder pads, it will stop the sound, but it's not going to change much. He said if it's still doing it after 500-1000 miles to come back. What they'll do then, other than tell me it's fine, he couldn't say.
Last week I had a flat tire on the way to visit my mother-in-law some hour and a half from home. Luckily, she's on great terms with the local Ford dealer and got me in to the service department (small town, everyone is family) as soon as I limped into town. I asked THAT guy the same question about the brakes and he said it's because Ford shifted to poly-alloy parts. The aluminum in the parts is mixed with other metals and they rub differently and wear differently and corrode differently than the old style brakes of years past. With a vehicle as big as the Expy-Max, it's going to be loud and there's nothing anyone can do short of switching out brakes for aftermarket ones which he didn't recommend. He said it's all in the name of getting the almighty EPA ratings...lower weight means better gas mileage. Welcome to the future and embrace the suck.
F that. I paid $80,000 for a car that squeals like a twenty year old Pinto getting dry-reamed by a Dodge? Screw the EPA and gas milage, these brakes are like fingers on a chalkboard EVERY SINGLE TIME I slow down.
But luckily, "there's nothing wrong."
(I will note that outside the brake issue, I absolutely LOVE this vehicle and there's nothing else I can complain about. At all.)