Sounds like you are building a Pygmy. The instructions usually call for you to fill a syringe and run thickened down the hull/deck seam from the inside after initially gluing the two together. Will you be doing that, or at least can you do that? If so, the thickened bead of glue on the inside of the seam probably will take care of it, darking the seam without first scraping out the original fill of clear epoxy. Also, if the area will end up fore or aft of bulkheads, the lack of light will cause the seam to look dark. Finally, you'll be surprised how dark even the perfectly clear glue in the seams is once the thing is all together. I can look inside my two Pygmys and see little lines of light along some of the seams. But you never notice them or perceive them as transparent from the outside.