The dowels don't hold it together, really. If you follow Tom's method of assembly, the epoxy holds the cross sections in place for the most part, lashings also provide most of the holding power; the dowels might help hold the cross section in place if the glue joint (or lashing) fails due to moisture or some other low-stress failure. If you hit something hard enough to break the epoxy, the small dowels won't add enough strength to keep the cross section from moving.

You could leave the "temporary" clamping screws in place so long as they were flush with the outside surface of the gunwales. They won't really add much (if any) additional strength to the frame, though. If the screws are not counter-sunk you'll have bumps along the gunwales that will invariably get scraped on all sorts of things, leading to accelerated wear of the skin at each screw.

: I am perplexed by the use of dowels to hold the boat together. Would it be OK
: to use countersunk or dome-head brass or SS screws? They could serve as
: both a clamp for the epoxy and a permanent mechanical fastener.