As far as the drag on the window when operated. I would think most of y'all have tinted windows. This contributes to the dying of the window lift motors and regulator failures. Keep both sides of the window rubber slick, like said with silicone.
As far as scratches are the inside or outside? Do you have tint on your windows. The best way to remove scratches from glass is a product called Micro-mesh. It is a product for aviation but works on all glass. It is time consuming but does work. I have used it many times cleaning aircraft glass, granted they were acrylic but it does work on glass.
As far as the alternator/battery questions, it varies hugely between manufacturers. Especially when you start dealing with Euro built cars. Remember an alternator produces AC power but your car uses DC power. Why is this important? Because of the identity of DC. Direct Current. DC draw on a battery is huge, your radio, lights and accessories not so much but when you start running DC motors the draw is tremendous. The amperage/current is much much higher with a DC motor compared to anything else in your car. I.E. running your window lift motors directly off of the battery. If your battery is old and weak running a DC motor can cause it to fail, especially if it is an older car because the older the motor the more it draws due to inefficiency. Motors get old just like us and use more energy when put into stress.
In other words your battery is probably OK for starting, which is DC, but continuous use degrades the battery over time, and using the lift motors will degrade your battery, also over time. My advice is replace your battery every four years. I have done this every since I came back from a trip out of town and the battery was kaput. No lights left on or usage, it just died due to sitting and I think all of the crap in the electrolyte shorted a couple of plates. JMO.
Karl