I don't think I've ever seen a potentiometer that wasn't sitting on a metal frame, that's why I didn't understand the extra wire, and the voltage split.
http://fddrsn.net/pcomp/examples/potentiometers.html
Potentiometer and description of operation. A would be 5V, B would ground, W would be connected to the signal.
This is exactly what a TPS is. For basic understanding you can think of a MAP as being the same thing.

Couldn't the ECM reverse the direction of current flow even if the windings had a common ground?
Yes, it could be done that way with added complexity. GM has chosen to isolate both ends of the stepper motor coil.

Is the 5 volt ref positive or negative?
It is positive.

Because of better and more engineering the the materials we used keep getting lighter and lighter yet carrying the same load.
Exactly. The 2015 and up F150 is primarily aluminum.

That's what you get when you buy a 72 year old vehicle with a 54 year old engine that's been sitting in abarn for 5 years.
If that's the only surprise then you've got a good rig.