So if one were building a new boat, would the answers change to the original questions?

I like to think about how a kayak may be abused, and build it with that in mind. So while you may only use the kayak every other week, dry it out after use and store it in a dry space, how would you build it if you used it daily, failed to dry it well and kept in the sun?

Plywood edge grain is very hard to seal. I might warm up the wood before brushing on warm, thin epoxy, then come back with a solid coat of epoxy thickened with silica. But before doing that, I might round over all the edges. Corners are where any sealant will fail first, so taking all of the frames to a router table with a round over bit would improve the life span. I might also sand all the frame edges and faces so there is no shaggy grain that might create wicks through the epoxy that might suck in water.

After the wood is sealed throughly with epoxy, I might give it another sanding, being careful not to burn through the epoxy, and then paint everything to protect the epoxy. Several coats of paint would be best, sanding between coats.

The amount of care you can take to protect the frame and increase the life span of the kayak is virtually unlimited. The question then becomes, how much effort is it worth. One of the beauties of fuselage frame is it is a quick, inexpensive way to make a boat, putting 20 hours just into rot-proofing the frame probably isn't worth it. You may not be making something you want to hand down generation to generation, so skipping a few steps probably makes sense.