If the glue line is indeed the weak point in these instances, my guess is that it is because the epoxy does not adhere as well to carpenter's glue or to TB as it does to the timber.

I agree with this idea. Perhaps this is another reason to consider Bjorn Thomasson's idea of glue-less stapling/pinning with epoxy added after stripping (but before glassing) ?

Woodstrip/glass kayaks and canoes should be quite stiff, and having too thin core (too-thin strips) is not a good idea, IMO. In my boats (these days) there's a glass bulkhead right behind the seat, and the glass/epoxy cockpit rim adds a lot of stiffness. If I could flex the boat in the cockpit area, I'd be very concerned. Actually, I have no problem sitting on the deck of my boats anywhere I want.
But, some would consider a 40 lb, 16 foot boat (with KS rubber hatches and adjustable footpegs) to be very heavy. Choices, choices.... ;-)