Etienne and Robs answer and your inquiry all tele the story of how vulnerable strip boats made of soft wood are - unfortunately.

I have covered areas like yours with stained varnish. Using multiple coats and a lot of patience I got it to cover very well. It's an art form that you learn by doing. Unfortunately when cedar stripers take a bruise, there's no easy sure-fire repair. if you sand it off, matching the color is almost impossible because the wood fibers are exposed and the sanding has to be identical as well as the epoxy viscosity and on and on. Thats why you don't see commercial boats with a transparent coating. The back transoms of boats have been natural for decades but nothing touches it(usually). At antique boat shows, you're not even allowed to breathe near the boats which have layer after layer of varnish on them.

I dod a few white spot repairs with magic markers. once dry i varnished over them. I would even fake the seam line with pencil and sometimes add in wood grain. But there's no easy way of just sanding the glass off without creating a mess.