This is very-very common with low profile, high performance tires. It is called "flat spotting". Completely reversible, once the tire comes up to temperature. Depending on the tire (brand, model, etc.) this flat spotting can occur in a day, a week, a month. Depends.
I own 2 Porsches and have seen this. When I hibernate the cars for winter, one thing I do to mitigate this, is to over inflate (per the Owner's Manual) the tires to approx 58 PSI. I also roll the cars by hand about 12 inches the beginning of each month (to change the resting spot on the tire). The last month of hibernation, I increase this interval to weekly.
With all this said, I've never experienced this phenomena with any of my Explorers (now on my 4th) in over 260,000 miles traveled. My 2011 Limited does not exhibit this, but it does not sit idle for more than 12 hours either.
With the combination of the 20" wheels, low profile tires (low for an SUV tires) and 6,000 pounds.....I can see why Ford is alerting the owners this MAY happen.