It is odd that tire change tools don't fit the car they came in. I'll check mine to see. It's not out of the question that different style wheels might have different size lug nuts, even if they are all part of the optional equipment on the same model car. It's quite possible that the factory has some bad information, production mix up going on and didn't sort it out till they heard repeatedly from customers and dealers about the problem long after cars left the assembly line. I.E. different nuts went on depending on the wheel type, but all cars got the same tool kit - even though a different lug wench was actually needed depending on the wheel and nut type.
Being a fairly new model, there's bound to be "ECO's" (engineering change orders) ongoing within Ford/Lincoln to resolve numerous production planning errors. TSB's are usually the signal that the company had gone back with sharpened pencils to resolve recurring problems and implement fixes before shipping more cars.
What's really a shame is that the dealer doesn't jump in and sort it out immediately so you're not left stranded somewhere unable to perform a routine tire change. But from all the posts here, sounds like most FoMoCo dealers are still learning what it means to provide really good customer service.
Hope it works out.