If it was a "bad thing" then why would the cumputer put the windows back up when you lower the top?

Try it. Top up, windows up. Lower the top but hold the switch beyond cycle completion with the tonneau cover latched. Your windows will go back up.

Logic would suggest it is OK. Your girlfriend, wife, (or both) will tell you it is required.
I wouldn't argue with either.

roadster with a stick