A small blemish like that can appear because of the glass going a a bit dry (not fully wet out) in that spot. Could have even been the cloth itself in the sizing (coating)?

A third choice would be to live with it and never look at it again. You can really open pandora's box trying to get it to wet out and match the other areas around it. If you must: wet sand the area with perhaps 300 git. If you sand into the cloth with the wet paper, you will see if the spot wets out with the water and disappears. Then you can epoxy on top of that and then varnish.
It's the best way of working on a spot like that because you can't destroy anything and the worse that can happen is it won't wet out. I found that wet sanding with even 600 grit into glass will wet it out or at least diffuse the light reflection so it looks wet out, works well.

Don't sand off the glass as you proposed unless you're a glutton for punishment.