im close to putting on the deck and would also like to hear the answer to this

will a little epoxy and wood flour fill in the gap?

i thought i had beveled the edges correctly (per the instructions) and they did not meet up 100%,  so i went with it, when i tacked the seams with the thickened epoxy, it filled most of the not perfect beveling.   

i think it is more of an aesthetic issue, than an issue of strenght.

Fill it in with a little Cabosil and epoxy, and by this time next week you'll have completey forgotten about it :)  I had the same concerns on mine and now have to strain to find out where the "gaps" are.   

Because the hull-to-deck joint ends up rounded over substantially with a sander, any gap or mismatch is going to disappear, literally turning into dust. 

While working on the prototypes, we tried fitting a Shearwater together with NO bevels just to see what happened.   I'm not sure you could really tell the difference between one built with all of the prescribed bevels or not. 

This tip should help when the deck and the hull have each been filleted along their seams, but not joined to each other.  When you prepare to join the deck to the hull, if you find that the deck edges stick out beyond the edges of the hull, or the reverse, try this:  Wrap a couple of straps or non-stretch rope around the boat (hull plus deck) in the area where the mismatch occurs.  Tighten gradually, manipulating the edge joint as you go; if the deck is slightly too wide, for example, the rope will bow it a bit more and pull the sides in.  You may need to reach inside and push the hull sides outward.  

This should pull the edges into fairly close alignment.  With the ropes or straps still in place, use clear packing tape or something stronger to hold the boat in that configuration.  Apply many pieces of the tape across the joint at right angles, along the whole length of the boat.  Make the tape pieces long enough to get good adhesion on both the deck and hull.  (Don't use duct tape -- the tape is strong enough, but the glue probably isn't.)

Now, fillet and tape the deck-to-hull joint.  The tape will come off easily once the joint is cured.  If you got epoxy on the tape, you may need to scrape off areas of the tape.

You may also want to use some copper stitches along with the tape during the joining process, but the tape works better, in my opinion.

Filler is good if you are painting only, the filler will show darker. On top of the seams, puzzle joints and stitches, it would look a real mess.

There is not enough 'meat' to correct by lots of outside sanding for roundover, it will be unsightly seeing all the layers of the laminated wood. Caution needs to be applied when sanding for roundover.

Just bevel and adjust the bevel until you have it right. Yes you already glassed the inside, you can bevel with the sander. Not a big deal to do it right and make it pretty. Just temporarily fit it and use tape or something to mark where you need more bevel for a better fit. Worth the extra time in the finished product. Don't rush it.