Grabbed from a PFF thread. Note that in the ALDL diagram at the bottom of the link, this is how it's installed under dash of most GM vehicles. In the Fiero it's located in the position TopNotch indicted, but it's turned upside down. Thus, the A and B terminals are on the bottom level, passenger side as you look back into the opening. Another thing of note is that the ignition should always be in the OFF position when inserting or removing your jumper. I've never tested the theory, but most say that it can blow the ECM if you do it with the ignition in the ON position. A big paper clip fashioned into a U works just great. Bring the car to operating temp, shut it off then start the procedure.
For your question, Ron, using the procedures in the link below, the ECM control of timing is disabled. With Winaldl you can do real time checks, so I don't know if it's disabled, but I would think not. With the jumper, you're setting timing at a static point, without any outside input, then when the ECM is back in the circuit, it adjusts timing based on sensor input.
Roger and Raydar have used Winaldl and certainly can answer your question.
http://www.obd-codes.com/faq/read-gm-2-digit-obd-codes-free.php