Tim --
In the third picture, it looks like at least some of the inside may have been rough sanded before the brown paint was applied, allowing the paint to soak into the sanding marks left in the soft cedar.
If you were to apply a stain, even a light-toned stain, to your stripped wood before revarnishing, it could lessen the visual impact of the remaining traces of brown paint. Old Town didn't stain the interior of its canoes (at least not usually), but other builders did -- notably Morris, who used a darkish, reddish stain -- so there is some precedent for staining a canoe interior.
Apropos of nothing, I have noticed that builders of other kinds of small wooden boats (dinghies, skiffs, rowboats, and small sail boats) very often paint the interiors of their boats even when new, rather than varnishing them, whereas canoe builders almost never do, although subsequent owners from time to time get out a can of paint rather than varnish when refinishing is called for..
I wonder why. Perhaps because the first canoes (birch barks) were not painted, and the bare wood look was just seen as the traditionally proper thing to do?
Greg