I would fill them first like the stitch holes.  That way there is no chance of an air pocket behind the glass.  The chines and deck edge are areas you may sand through very light fiberglass so better safe...

yeah, thats what I thought.  But wait, did you fill your stitch holes prior to glassing?

Yes, I swiped each stitch hole with a filler mix and then sanded the surface back smooth.  I did the stictch holes, chines, transom, hull seams, etc. as the last thing before glassing the board.

I think avoiding any type of air pocket behind the glass is a good idea. the glass supplied with the kit is very light weight.  Sanding through it is easy to do anywhere there is an edge, a ridge or air pocket.  Also trapped air could expand creating a pin hole if the board got really hot in sun.  So I just made sure the surface was sealed..