In most cars you do not need to do a 2 step programming so they can simply program the unit on their end and send it to you. In the case for the focus it goes like so.
1. Program part one on computer
2. Plug into car turn ignition on (light on box flashes rapidly and stays that way)
3. Remove box from car plug back into computer and program for part 2
4. Plug back into car and turn ignition back on, wait and light will go solid green.
And yes the factory ford one is a POS they use and extra key in a box. I seen the diagram when I first got my car and refused to do it. The diagram from Idatalink is doing exactly what you would do to start the car 1. shows the key present, holds the brake, hits the start button, lets go of brake. The benefit of this is when the dealer plugs in with the scan tool there will be no codes present from modules not being power up properly.