I have an SVT which came with the "premium" sound system. The power antenna goes down whenever I turn-off the head unit (though not when I am using the CD player). If I turn-off the head unit, it retracts despite the fact that the car's ignition is on. It has always and still does work this way even with my current aftermarket head unit.
If you take out your headunit, you will see a green lead feed into the radio . . it is the wire for the power antenna. There are also red wires for constant power and an (orange?) wire for ignition power (in addition to some other ground and dimmer lines). Somewhere along the assembly line, I wouldn't be surprised if somebody crossed or mixed-up the wiring for the power antenna with something else like the orange ignition power lead.
Alternatively, if the antenna does go down when you turn-off your radio, the problem may possibly lie with your factory radio, and will probably rectify itself when you install your aftermarket head unit.
If this isnt't the case, and/or your antenna still doesn't go down when you want it to, you can always manually bypass it by installing an in-line switch along the green lead (you can get one from Radio Shack pretty cheaply). Even though mine doesn't have a problem retracting when the radio is off, I installed a bypass switch nonetheless so that I could retract it when I am listening to CDs and not the radio.