I faced the same issue on my MC 16.5, except I painted the cockpit.  Before installing the deck, I masked all the surfaces that would be epoxyed to the deck, coaming, or anything else (top edge of bulkheads, deck beam, sheer clamps, top & inboard side of carlins) and then painted.  I was concerned about painting the underside of the deck which had to go on with wet epoxy, but would be very hard to reach after installation.  The advise from John Harris was "don't worry about covering the expoy on the underside of the deck".  So, that is epoxy only and all the rest of my cockpit is well covered with one coat of primer and two finish coats of paint.  After painting, I kept the interior lined with plactic drop cloths to keep epoxy dribbles off the paint while installing the deck, coamings etc.  My upcomming project is a Shearwater 17 Hybrid and I will try to figure out a similar approch to that one.  You can see my MC, including a cockpit picture, under Paul G in the CLC Mill Creek main Gallery.  Smooth Sailing

After finishing my Shearwater 17, I rough sanded the inside of the cockpit and brushed on a single coat of varnish.  It's not as shiny as the exterior, but looks good and gives a finished appearance.  I had no problem reaching any part.  I did not varnish where the seat would be glued on.