In the realm of stitch & glue, whether rabbeted lapstrake or other configurations, I've heard it said that "1/8" is 'close enough'" given the ability of augmented epoxy to fill gaps and create structural elements where there was nothing before.

Still - and I admit here that I'm a first-timer with my Waterlust project - in one's enthusiastic progress it's easy to overlook the simple truth that sometimes going back to re-evaluate what's been tightly wire-stitched is a necessary step.

As with any assembly of parts, often the only way to get everything to fit properly requires not tightening all the fasteners fully as you encounter them. Rather the idea is to get everything loosely secured then gradually work the fasteners down snug a little at a time.

There's no shame either in exercising creative applications of what's at hand to move things into position - clamps, weights, levers, blocking, 'spanish' windlass, etc. - whereupon the stitches can then be drawn tight while the other arrangements are doing the bulk of the positioning. 

   The Skerry is a double ender also that suffers from this during build time.  In class we were able to reduce the gaps when we flipped the hull upside down and started getting all the ties tight and everything squared up but there were still gaps.  Basically we use huge fillets at the bow and stern inside and then round over the outer edges and it gets fiberglassed.  Structurally you won't have anything to worry about but I have seen people frustrated with the kit because they wanted to do brightwork on the outer hull and it doesn't look super amazing (Doesn't look bad to me but to each their own).

My own boat has a spot where light comes through at the very edge of the large fillet and the breasthook I need to fill in with something, though im not worried about in structurally just a bit weird looking if you put your head under the breasthook and look in there.