The factory harness has 8 slots - 4 on top and 4 on bottom. There are only 4 wires, all across the top of the harness. The 4 slots at the bottom are totally unused.
The aftermarket harness also has 8 slots, 4 on top and 4 on bottom, but it uses some pins on the top and some pins on the bottom.
It's not a matter of unused wires. It's a matter that the used wires don't match up correctly. For sure, Ford changed something on the audiophile system of the 2007 Edge. It's not the same as previous model Fords with the Audiophile system.