A reasonable concept, but I fear implementing your idea will cause problems with how the mast installs. Mainly the mast step would now be enclosed within the seat box. Not an insurmountable problem, but you'll need to think it through once you get the hull built.

   It would be easy to build the seat/bench to keep the mast exposed. Picture a slot or channel in the seat. The Mast step would be in the open with the bench on either side.

   I have been thinking about the same issue as I build my NED.  Not sure if you have seen the below video of the NED being intentionally swamped with the floation installed per the instructions.  What is clear is that in anything but a flat calm body of water, it may be difficult if not impossible to re-enter the boat and bail enough water to be able to sail/row away.  I sail mostly near-shore in the ocean where even moderate waves could be problematic.  I personally believe making the stern seat water tight and adding flotation in the bow would provide enough buoyancy to keep the boat sufficiently above the water line to be able to bail and regain the ability to sail/row.  Enclosing the two middle seats to make them watertight might provide two advantages.  First provide a larger buoyancy chamber without adding any weight.  Additionally, by adding a watertight access port would allow that space to be used for some storage.  I would do the same in the bow.  Below I have added several photos of ideas which I may incorporate.  I particularly like the one with the Mast.  This set-up would be adaptable to either the lug [and eliminate the piece that spans the boat, which I consider to be an eyesore] or the sloop rig.  Keep us posted on how you tackle the issue.

https://youtu.be/cCwRUwG7JbI

I have seen the bottom picture before, it is not exactly what I had envisioned but pretty darn close. If I understand what you are saying, you believe that just having a sealed water tight enclosure would trap enough air to add the needed buoyancy? I will only be sailing on freshwater lakes. Maybe once in a lifetime would I be able to take my boat to the ocean.

O.K.  This is not going to make a lot of people happy, I fear, but it seems that it should be said nonetheless.  Before getting to that item, preface my statement by saying that I'm within a few days of finishing my NE Dory hull.  (The interior is done and one more coat of primer and three of color on the exterior and she's ready to hit the water.)  I opted for foam insulation reinforced with epoxy, painted a flat black, and installed under the thwarts as described in the construction manual.  As John says there, the soft black of the floatation next to the brightwork (rails, thwarts, and hull) looks really good, really shipshape.

That was the easy part.  The hard part comes from stating the obvious:  For thousands of years, wooden boats have put to sea safely without any floatation at all.  My Dory is the first boat I've built, but I've owned and operated a lot of others, ranging in size from a 9' sailing dinghy to a 44' racing sloop, and from a 12' crabbing skiff to a 37' trawler.  None of these had any extra floatation.  Do bad things happen at sea?  Absolutely.  Does the prudent sailor prepare himself properly for all eventualities?  If he's any good.  So adding some floatation isn't a bad idea -- and making sure that you have a good life jacket and you wear it all of the time is a better one!  Beyond that, you can modify all you want and take great joy in building stuff -- many people seek nothing more -- but I wouldn't get too wrapped around the axle about how much "extra" floatation I had or where I was going to put it.  Chances are you aren't going to be single-handing it around the world, but rather playing with it in appropriate waters.

Those are just my thoughts.  

O.K.  This is not going to make a lot of people happy, I fear, but it seems that it should be said nonetheless.  Before getting to that item, preface my statement by saying that I'm within a few days of finishing my NE Dory hull.  (The interior is done and one more coat of primer and three of color on the exterior and she's ready to hit the water.)  I opted for foam insulation reinforced with epoxy, painted a flat black, and installed under the thwarts as described in the construction manual.  As John says there, the soft black of the floatation next to the brightwork (rails, thwarts, and hull) looks really good, really shipshape.

That was the easy part.  The hard part comes from stating the obvious:  For thousands of years, wooden boats have put to sea safely without any floatation at all.  My Dory is the first boat I've built, but I've owned and operated a lot of others, ranging in size from a 9' sailing dinghy to a 44' racing sloop, and from a 12' crabbing skiff to a 37' trawler.  None of these had any extra floatation.  Do bad things happen at sea?  Absolutely.  Does the prudent sailor prepare himself properly for all eventualities?  If he's any good.  So adding some floatation isn't a bad idea -- and making sure that you have a good life jacket and you wear it all of the time is a better one!  Beyond that, you can modify all you want and take great joy in building stuff -- many people seek nothing more -- but I wouldn't get too wrapped around the axle about how much "extra" floatation I had or where I was going to put it.  Chances are you aren't going to be single-handing it around the world, but rather playing with it in appropriate waters.

Those are just my thoughts.  

Don’t worry I’m happy! Everything I have been talking about is purely speculative so far. I haven’t yet received my kit or been able to review the manual. I just happen to have one of those disturbed brains that has to poke at things. As I said in my first post, I will most likely go with the foam under the thwarts as you describe. If that is what CLC recommends that’s probably what I will do….but it never hurts to check all the options out. Thanks for everyone’s input and feel free to keep it coming!    

  MountainSailor  I have no issues concerning your comments. Like you I have sailed all my life, including ocean passages on my 32' wooden yawl, which I no longer have. Floatation in boats is a relatively new concept to enhance safety.  The Coast Guard, states, all boats made within a specific size limit, and with outboard engine are required to float level when totally swamped, for a PERIOD of time.  That time is usually 24 hours.  On small production sailboats built today, most are incorporating either floatation, air tight compartments or room for floatation bags.  I suspect the thinking is an ounce of prevention...etc.  On the other hand, I visited my son and daughter-in-law in Copenhagen this summer and found a large number of beautifully crafted wooden sailboats without any floatation [see pic].  In my case, since family members will be using my boat, who are not as experienced as I,  I want to ensure that in the unlikely event they capsize, they have the ability to re-enter the boat, bail it out and resume their journey.  As a side note, we never leave shore without life jackets, a handheld VHF radio, and a PLB. 

Hey check this out!

http://www.clcboats.com/life-of-boats-blog/team-dory-build-at-clc.html   

   NOW THATS WHAT I Am TALKING ABOUT!

My Dory is well underway now. I am attaching the 2nd set of rails tonight. I have never stopped thinking about making watertight compartments fore and aft to replace the foam floats. One of the little details that is worrying me is I will have to make supports and bulkhead extensions to create the front compartment. I don't have access to Okoume ply. Since these will just be small supports, and completely encased in 3 layers of Epoxy. Would I be able to get away with cabinet grade plywood? Since its not a structural member and would never touch water, I can't see why this would be a problem.

   My dory is used for 2 seasons at the Jersey shore and only sees saltwater. I used interior grade plywood from Home Depot to make a raised floor board in the bow compartment. With 3 coats of epoxy and now 5 coats of paint, there is no signs of water intrusion into the plys. The bottom is not painted so I can see the wood. I've had cracked inwhale spacer blocks that turned black very quickly where water soaked in. Good epoxy coating will keep you watertight.  I followed CLC's thwart flotation instructions and painted the epoxy covered foam flat black against a hatterus white interior. I hope to never have to test the need for the thwart floatations but it is there if anything does happen. Happy building. Dan

   Dan, how about a photo or two?  We would love to see the finished project...