PCM controlled. Because of the factory dual alt setups, the PCM chooses between 2 different wires to excite. In single alt trucks, there is a "loopback" in the plug on the passenger side inner fender. That loopback completes the circuit to the single alt if the PCM chooses the second alternator. If you want a second alt, just mount it up and get the harness that goes from the alt to the plug on the inner fender, remove the loopback and plug in the harness...done.
You probably could wire the alt to a key on, but the factory setup seems to work fine.
I believe that the jump from 11.5 to 14 volts is happening when the GPs shut down and are no longer drawing on the electrical system...but I could be wrong. Not sure how the alt would like being asked for full output on cold startup with the GPs at full tilt...it might shorten the life of the alt and it might be easier on the alt the way it's coming online now.