I thought I would post my experiences in case they can help another Mini owner.

Normal Glass Cleaning
I usually just clean my windows with a quality glass cleaner and newspaper. I've tired many brands; my go to cleaner is Stoner Invisible Glass. This usually does a very good job and doesn't streak.

Removing Water Spots From Glass
I tired to clean the glass using Invisible Glass on my just purchased used 05 convertible but water spots remained behind. And most of the spots were on the inside of the windshield!

So I tried using straight (not diluted) white vinegar as some have suggested. It didn't do a thing.

So I bought a product called Spot-X Hard Water Spot Remover. This did the trick! I like it because they include the non abrasive pads and explicit instructions. You can actually feel the product cut through the spots and you don't have to wear gloves. And it didn't scratch the windows. I have enough left over to clean the windshield another dozen times.

My Previous Experience with BMW/Mini Glass
I find the Mini glass to be softer and more porous than other autos. Is it just me?
On my 2008 MCS, the rear window became scratched accidentally by me when I was scraping off snow and ice! The scratches looked like cobwebs on the windows under certain lighting conditions. I should of used the defroster and not tried to speed things up. Live and learn.