What you are calling a "foot throttle" is not a throttle at all. It is the hydrostatic control. Like mentioned above, the foot pedals control the stroke of the hydrostat's piston pump. Auto Throttle is really called eThrottle (the John Deere name)
Just think of it like this: As you press the pedal down, the transmission shifts into higher and higher gears, so the ground speed keeps increasing whereas the engine RPM doesn't change, although the engine may "lug" a bit. Of course, there are no gears...It's a variable displacement piston pump feeding a fixed displacement hydraulic motor. So the pedals (via the computer), control the angle of the "swash plate" on the piston pump. The steeper the angle, the more fluid is moved (per pump revolution). The hydrostat pump is coupled directly to the engine...if the engine is spinning, so is the pump. The 3 range gearbox is connected to the output of the eHydro's hydraulic motor. This makes the tractor more useful, and keeps the hydrostatic transmission's system pressure within practicle limits (about 5500psi max).
With the eThrottle system, the computer just looks at the pedal postion, and increases the engine RPM accordingly. eThottle is really nice for loader work, especially when used in conjunction with LoadMatch.
The main "take away" is that the pedals control the amount of fluid that the pump is moving, thus the ground speed.