Stop! Before you go any further, I strongly recommend you read Kayaks You Can Build by Greg Rossel and Ted Moores. Firstly because I believe they address this specific question. But secondly because I wish I had read it BEFORE I started on my dory. If for no other reason read it because it will reduce the amount of sanding you do by a huge factor.

   Your mention of a dory reminds me that in building the Northeaster Dory I did not put cloth on either side of the puzzle joints. The manual just calls for them to be glued and clamped. What's more, cloth only covers the puzzle joint on the lower-most strake. The top three strakes are joined only by epoxy forever.

My dory has been plenty strong, thriving under plenty of hard use. Why would the kayak need such different treatment?

 I believe that you would be fine as long as the joint eventually get covered with cloth.  On the S&G Petrel and Petrel Play builds, the manual does not even call for epoxy when putting the puzzle joints together.  You use CA glue to hold the puzzle joints together while stitching the boat.  After it is all wired up, you use dots of CA to hold the seems together.  Then you cut all the wires prior to filleting.  The advantage to this approach is twofold.  First, you can hold the puzzle joint (or seam) perfectly aligned while you lock it in place with a dot of glue and a spritz of accelerant.  Secondly, removing the wires allows you to have much smallerr fillets.  Here is a pick of the deck of my PP with only the CA glue holding it together.   

It may add some extra support to the joint until more glass and resin is applied. This could also be a carryover from the use of scarf joints that could pop apart on a sharp bend.

Also from before puzzle joint technology was worked out and had its reliability established.

Laszlo