This comes up quite often on the BB. With a S & G boat you might be tempted to fill the stitch holes with epoxy putty or wood filler or something like that. The main problem is that when you contaminate the surrounding area you will get a noticeable color difference and it will look terrible - much worse than any staple hole. If you try to sand the area after filling them, the sanding marks will do the same. There is no easy way of matching the surface of the veneer with any sanding. With a stripper, you can drive in a little wedge of the same wood and nip it off with a cutting pliers. (no sanding or glue) When you wet out the wood with epoxy, it will get darker and the holes will hardly show at all. When the boat is dry and unfinished, the contrast of the dark holes is greater and disturbs some builders. All of this assumes that you are not painting the boat but using a varnish.

The reason you manual did not address filling the holes is because it always leads to disaster.