pribs67,
Tech articles are always good, as you never know when you will need the information.
I would have a look at the auto-up function for the windows, as I've only seen this done recently on some newer high end cars. The reason is that if anything is sticking out the window when it goes up, you run a real risk.
Personally, I would just wire them up normally and have the alarm wiring separate so that I could leave the windows down a crack in the summer to get some air circulation. It's not like a VW is secure anyway, but this may just be me talking, as I have a couple of VW Cabrios. Nothing like a good piece of canvas to keep the thieves out.
Doug