I don't think there is much you can do aside from scraping if your tank is currently set up.
Next tear-down, try wetting a paper towel or napkin with vinegar, sticking that over the area, and let it sit for a while, then go at it with the scraper.
Vinegar should work for carbonate stains, if it's not, then the glass may be etched. I haven't seen it myself, but I've heard that after a while, sometimes the glass gets etched where the water level is.
I think I've heard people recommend using cerium oxide, but I don't know anything other than that.