The problem with polishing out a scratch is it usually makes the vision through the glass distorted. That may not be a problem in a side window, but it is in a windshield. I had the windshield replaced in my Wife's Pontiac Vibe, and as soon as she sat in the car, she started complaining that the windshield near the bottom was distorted. I'm just under 6 feet, and I never noticed it, she on the other hand, is 5' 2".
I ended up taking the car back and the shop owner agreed that the bottom of the windshield was distorted, ordered another piece of glass, and replaced it at no cost. He explained that being so low that the supplier probably polished a scratch in an effort to save the new glass. I felt bad that he had to redo it for free, but he told me that the supplier made it right with him, so he wasn't at all upset about having to do 2 installs.
All the polished glass I've seen done, does usually leave a visual distortion where it's done. If you're fine with it in a non critical area, then it's of no problem.
