My first CLC build, a Sassafras, was ages ago, and the directions at the time had me  put in the complete fillets over the stiches.  Afterward, I pulled the stitches with the aid of a little heat on the wire from a soldering gun.  They all slid out fine.  The later ones, like my skerry, had me put in initial "tack weld" small fillets between stiches and then remove the stiches before putting the complete fillets in place.  I don't know the peapod details, but either way could work.  Maybe there's enough twist and tension in those joints that they are cautious about having you do the tack welds to hold it, and figure it's best to hold everything with stitches until it's all together.  You can get the wires out either way.

   I believe p61 in the manual indicates the stitches are supposed to stay in place until the stem & stern fillets have cured. Could you make bigger fillets to avoid the wire to interfere with the glass, without causing pain to the eye? I would not say your alternative approach (tack-weld the outside) is impossible, but certainly more risky to have the panels pop. Certainly I would not glass over visible wire.

The stern and bow fillets & glass are  explained on pages 56 & 57 and the photos show no wires whatsoever.  That's what makes me think it's out of order.

I don't feel like a larger fillet is the solution since the stitches that hold the planks at the edges would still be in the way of the fiberglass glass tape that's to be laid into the fresh fillet.

The issue for me isn't the bow and stern stiches themselves; it's the stitches a few inches back from the V that hold the plank edges.  That's why I'm considering the jumping ahead to tack welds of the planks and removing those plank-edge stitches (while leaving the bow and stern stitches in place until the bow & stern fillet cures) and then doing to bow and stern fillets.

   Call or email CLC directly.  They are great folks for tech support. I actually had some real quirks with my skerry.  A recent update of the CNC files had caused a mirroring of some slots in the bottom that had me stumped.  John got right back to me and straightened the confusion.  

OK, I understood it was about the stitches right at the V (side note, I don't have the kit here, only the manual; building a Chester Yawl, though). I would say it's ok to do the tack welds then and remove those plank edge stitches, as the tack welds are supposed to be much stronger than the copper wire. Beyond this, I totaly agree with Mummichog - if in doubt, call CLC. Absolutely best option for peace of mind.