Many dealers do clean the throttle body. They recognize that the teflon coating does cut down on the gunky build up, but doesn't really prevent it. Before Ford introduced the teflon coated throttle bodies, cleaning was even more essential. After they started the teflon treatment, Ford would no longer pay for cleaning under warranty.
Ford has also converted to DRI (Deposit Resistant Injectors). Before converting to DRI, injector cleaning was also more critical. They also claimed that cleaning injectors was no longer necessary. It did help, but they soon backed away from their attitude of "never needs it anymore".
As to what is causing your check engine light, it is all speculation until you read the codes and check it out. Literally hundreds of things can trigger a check engine light.
