In my cab, only the front windows go up when I put the top down. In some cases, I can't remember when, the windows don't go up at the end of the top-down cycle. Lately I've had a problem with trying to raise the rear windows after the top goes down. They just don't respond to the switches. But other times, they go up fine with the switches.
I'm a big fan of the SmartTop and use it a lot, primarily when leaving the car in a parking lot and when I return to it. The tilt-mirror function is redundant with the sport chrono/power seat option. I do like the delayed open for the frunk release though.

 

I think I need one now!