Definitely would not trust anything the dealer says at this point, including that they have actually talked with Ford. If you have an option to take it to a different Ford dealer, that's what I'd do next.
I have a 2018 mustang GT with the 10R80 trans, and it almost always skips 2nd and 4th gears. Occasional hard downshits around 4 to 3 when cold. Otherwise very smooth.
What is the difference between the 10R60 and 10R80?
Some dealers don't care, they just charge the cost off to Ford corporate. I would contact Ford cust srvc and tell them your issue and the dealer reply.