What's classic is that you're not looking closely enough - there's another wire in C106 shown in the diagrams. And the note doesn't say C106 isn't used; it refers to that one WIRE not being used in Ls. C101 is made onto the HVAC harness, which is common to all gas trucks. And Ls may not have that wire in the engine bay harness, but they have the other, so they have the connector.
But your question DOES raise an interesting point... In most Ford diagrams, wires that pass through the same connector are generally joined on the diagram by dotted lines (like C101 in most of them). So I may re-draw those to make C106 more-apparent...
It doesn't do anything in a Lightning because it's not used. Your question still doesn't make sense. In other trucks, it tells the EEC if A/C is requested. But Ls are apparently programmed not to need that input.
What motors? There are no motors connected to either wire that passes through C106. One is clearly shown going to the EEC/PCM; the other connects the low cutout switch to the clutch.