Actually, there is a switch in the windshield head liner that, once you turn the handle, tells the BCM to lower the windows and tells the TCM that you have unlatched the top.

Then, the switch you disabled works in series with the switch in the trunk - if the trunk divider is deployed AND the switch you bypassed is closed, the pump is allowed to run.
THe purpose of the switch in the trunk is, of course, to assure that the divider is positioned properly. The switch you bypassed is to assure the top is released completely from the windshield frame. That is, it assures that the top is "pushed up" from the frame and is ready to fold properly into the storage area.