There might be some slight kernel of truth. A Ford/Mercury PCM is programmed in one of three ways.

1. With the old PCM installed connect the scan tool. When the scan tool connects to the car it sucks out the build information of the vehicle. A PCM replacement is the initiated in the scan tool and the scan tool will tell you when to install the new PCM. Once the new/replacement PCM is installed the scan tool will push the programming into the PCM. This is the easiest way to program a PCM. Since you have already installed the PCM this method was most likely not used.
2. If the old PCM is damaged beyond being able to retrieve the build data the build information needs to be reconstructed. One way of reconstructing this information is from stickers on the PCM. The numbers on those stickers are typed into the scan tool and it will assemble the build information. If this method was used for your car the numbers on the PCM may have indicated a manual transmission.
3. If the old PCM is damaged beyond being able to retrieve the build data the build information needs to be reconstructed. The dealer has assess to a system that will give them every build number associated with a particular vin number. By then sorting through the list, the build number can be selected that matches the vehicle options. By typing the numbers into the scan tool the scan tool will assemble the build information. This method should have been used because the old PCM is not available and the stickers on the PCM may not match the vehicle.

There might be some slight kernel of truth. A Ford/Mercury PCM is programmed in one of three ways.

1. With the old PCM installed connect the scan tool. When the scan tool connects to the car it sucks out the build information of the vehicle. A PCM replacement is the initiated in the scan tool and the scan tool will tell you when to install the new PCM. Once the new/replacement PCM is installed the scan tool will push the programming into the PCM. This is the easiest way to program a PCM. Since you have already installed the PCM this method was most likely not used.
2. If the old PCM is damaged beyond being able to retrieve the build data the build information needs to be reconstructed. One way of reconstructing this information is from stickers on the PCM. The numbers on those stickers are typed into the scan tool and it will assemble the build information. If this method was used for your car the numbers on the PCM may have indicated a manual transmission.
3. If the old PCM is damaged beyond being able to retrieve the build data the build information needs to be reconstructed. The dealer has access to a system that will give them every build number associated with a particular vin number. By then sorting through the list, the build number can be selected that matches the vehicle options. By typing the numbers into the scan tool the scan tool will assemble the build information. This method should have been used because the old PCM is not available and the stickers on the PCM may not match the vehicle.