What? If you fully retract it and then screw the IAC motor on, the pintle will be forced to screw in against a very high gear ratio (stepper motor), which can damage things in a hurry. Maybe we misunderstand each other in terms of what "retracted" means. I mean you turn it all the way in by hand so the assembly is as "short" as it can be. You turn it all the way in so it doesnt interfere with anything. Then you jump those ALDL pins, (without starting your engine) and the computer will drive the pintle forward until it seats, and will then sense that it has bottomed out, and will stop sending voltage to it. The computer now knows the position of this motor, logs the position, zeros it out, and uses that zero point to know where the pintle is. The number you see on your scan tool, like "25", means the stepper motor has stepped out 25 increments. Pulling the pintle all the way out and then screwing the whole assembly into the TB will put alot of pressure on that pintle, and all the gears inside that will have to spin backward. I deal with stepper motors here at work all the time and know what never to do to them. You never force them to spin by hand in a direction that could damage the gear assembly. These IAC's fortunately are designed so that they can be rotated inward without putting force on the gears.
Ive read people on here calling the TPS sensor a stepper motor. Dont know why they would say that. The TPS is a rotary encoder (another thing I deal with in our designs and products). Encoders usually use a quadrature signal to determine position.