My brother did the same thing. He sanded into the veneer on the side of the cockpit where you do that butt joint. He chose to do nothing. The boat is about 5 years old and looks the same. The varnish gets darker with age, but not magically in that one spot.

The reason the veneer is lighter when you sand into it is because you are exposing wood that has not been exposed to oxigination. Since plywood is stacked it's not UV that is causing the color change. The plywood also has a coating of dust and grit from handling which makes the skin a little darker than fresh exposed wood. Most people don't sand new okume plywood before epoxying (there's no reason to). Plus the varnish you use has UV filters to protect the epoxy.

In another spot, my brother sanded through the veneer into the core. It was really noticable and bad. Here we used the staining method I described. It worked out pretty good hiding a bad mistake.

You can experiment. If you don't like it, wipe it off with a rag and some thinner. Good luck.