Hi gespliesste,
I'll take a stab at this...
You don't HAVE to use Flexcoat. Remember that glass rods were transitional rods. Coming after bamboo and before boron and graphite. The transitional makers were still using varnish on their wraps. Yes, you can sand varnish. I had a friend who would turn flex coated wraps down on a lathe. They looked just fine! I'm not suggesting you should do this but I think the key to this is the final sanding with a grit so fine the the very last coat you put on it doesn't show the sanding scuffs below.
And yes, I would say that you wouldn't want to scuff the actual glass. Protect it with a wrap of masking tape. If you sand and scuff through the tape, peel it off and stick a new wrap of tape on it. Don't be overly aggressive.
Oh and any of youse guys still making glass blanks that might have taken exception to me calling glass rods "transitional", my apologies! It wasn't my intention to offend. In fact I think that glass rods are the next best thing to bamboo!
Mike