Powertrain warranty coverage is only on internally lubricated parts. The Throttle body assy is not internally lubricated. The motor that you are talking about is part of the throttle body assembly.
The transmission control module would also not be covered under that warranty, unless it was inside the transmission.
The throttle body on that vehicle is controlled by the engine control computer. Unlike throttle bodies of the past, the modern vehicle (pretty much all modern vehicles, regardless of make are or have gone this way) does not use a throttle cable from the gas pedal to the throttle. It is controlled by wires and electrical signals from the computer only.
I don't know if you have contracted Ford Motor Company as yet, but keep in mind that the dealership is NOT owned by Ford. They are contracted by Ford to perform repairs on the vehicles and when under warranty, Ford pays the dealership for those repairs.
The dealership has to follow very specific instructions from Ford as to what can and what cannot be done. If a vehicle is outside of the 3 years or 36,000 mile warranty period (which ever occurs first) the Ford Motor Company is no longer required to pay for any repairs on the vehicle. If you have a service contract (an extended warranty) then the coverage extends to that warranty. But if the part that has to be replaced is not covered by that warranty, then the owner of the vehicle is the person responsible for the repair.