I also built a Pygmy and I recall the discussions Jeff mentioned. Some folks did say they sanded off the tape on the outside. I choose to leave mine alone though (I also think it might be structurally important), and the joints do have color mismatches. It's backward from the way your hypothesis would have it, though. The color at the joints is lighter than the rest of the panel, not darker. One explanation I've heard is that unepoxied wood darkens due to oxidation. The seams are epoxied first so they darken least. Pygmy's manual even mentions it in the construction manual. Makes sense to me. After varnishing, the color difference is hardly noticable on most of the joints and doesn't bother me a bit.

: I think you have misinterperated an earlier discussion. The tape on the butt
: joints is structural and important. My hunch is that someone did not sand
: before they put the tape and epoxy on the joints which would make the
: unsanded wood darker then the recently sanded wood on the remainder of the
: boat. The solution is to sand before you tape not sand off the tape. You
: will never have a perfect color match in bright light if one area has more
: layers of glass than another, but it should be close.