Windows

You can, but they will crank in or out with the vibrations of the wind. If you have a cover (like an Air Max) over your roof vents, you'd do better to leave them open. If you don't have a cover, they too will vibrate in the wind, and eventually crank open or closed.

I've not seen anyone towing their trailers (TT or 5er's or Toads) with windows open.

I once transported a car for my daughter from Indiana to Charleston, SC, and had to leave the sun roof open to get out of the car. Oh my, what a mess when we got there.