Definitely coat them with epoxy and forget about a varnish finish on that part of the boat. Paint is your friend, it covers a multitude of sins.

It looks from that image that the joint was not flat since the fingers on one piece of wood are sanded entirely through the first layer and pretty deep into the second while the other piece looks normal. i suspect that the back side of the joint is just as bumpy, right? Because of that there may be some structural issues to fix as well. Fortunately, it's easy.

On the back side, get rid of the bumps by either sanding it the way you did the front or filling the low spots with epoxy/woodflour and then smoothing it. Then put a piece of fiberglass over both sides of the joint, front and back. It should be relatively heavy cloth. I'd use either a single 6 oz piece or two 4 oz pieces on top of each other.  The glass should be as wide as the joint plus 2 inches on each side of the fingers. Do that on each side. If you use 2 layers of 4 oz, make the bottom layer 3 inches on each side of the fingers. Thay will let you smooth the patch more easily. WIth one heavy layer you're going to have to feather the edges.

The glass patches will more than restore the strength you lost by grinding away the veneers. Done carefully and with good surface prep for paint it will be completely invisible under the paint.

Good luck,

Laszlo

   Sometimes you just have to press-on like you planned it that way. .....or paint the hull. ...or cover it up. Or start over. (Naw) . I would proceed as of i planned it and consider a cover up. It would be delicate with thin plywood or cedar but I might consider flame scorching a pattern. ..Like it was too fast??😉

   Too much flame / heat will discolor and weaken the epoxy.

   I did the same thing on the puzzle joint in the rear on the side panel on my Shearwater 17 build.  CLC sells some wooden inlays/onlays.  I am thinking of getting one that will have my boat name and the year I built the boat to cover it.  Your area looks larger and I am not sure where it is, but I want to throw out the idea as an option.