Yes, the clear coat looks like it will do the job.
If you really want it to look good, take some 150 grit abrasive
cloth and rub the damage until you start to see a little wood.
You just need to open up the area so it can dry thoroughly.
The wood is supposed to be soaked with a specific amount of
epoxy when the board was made, but due to differences in the
wood sometimes certain areas don't soak up as well as the rest
of the board. I think this is the case with your board.
Just open it up to the air, put it out in the sun to dry and bleach
a bit, then coat with the Clear coat.
This is a cosmetic thing only. The water is not getting any further
than the thin layer of wood on the surface.
Hope this helps,