Sean,
I don't know what kind of varnish they used when they built the
boat. When it came time to refinish my
interior, I took the old finish off completely, right down to bare
wood and put 5 coats of HelmsmanŽ Spar Urethane on. You've seen the results.
The procedure for your particular situation is to sand around the scratch, right down to bare wood. Then grab a wet face towel or any material that holds moisture and with a hot iron , steam the scratch through the towel. If not too deep the wood fibers , in the scratch, should swell and level the area. Lastly, unfortunately, I doubt you can match the finish with a spot varnish. You will probably have to at least rough up and varnish a large enough area that the 'spot' blends in.
Or..... just slap a new finish on top of it and hope for the best.