I typically left the top of my '88 unlatched so that I could open / close it from the remote control. I also had Clifford SmartWindows II modules on both the front and rear windows. The whole system was pretty slick -- arm the alarm and the front windows closed, then the rear windows closed, finally the top closed. Since this took about 20 seconds to complete, the system would also bypass all of the sensors to eliminate the top triggering the alarm. Disarm, and within 10 seconds press the aux channel and the front windows lowered, then the rear windows lowered, then the top. If you're worried about making it easier for a thief to get in your car, then just realize that they'll cut the top before they try the door handle. I installed some micro magnetic reed switches on both sides of the top part of the windshield frame that would trigger the alarm if the top was pulled back.
If you were REALLY ambitious, then you could set up some pneumatic solenoids to open / close the latches. In my opinion, this would certainly not be worth the effort. btw . . . I still have a pair of SmartWindows II modules with harnesses too . . .