I don't have a whole lot of direct experience on this but in a previous thread Bubblehead made a comment about filling stitch holes with a mix of both cellofil and wood flour to approximate the okume color. Perhaps that could help in your case. I experimented with this a bit and found that 2 parts unthikened epoxy plus 1 part wood flour and 1 part cellofil creates a decent color match. It's not perfect but it did help blend my stitch holes, a couple panel gaps and one unsightly gash I made in the middle a shear panel with my utility knife (I accidentally cut into it a bit when zipping away the excess fiberglass hanging over the dried hull). For that latter case I was surprised to be able to blend the filler so evenly in color that is almost disappears into the grain pattern of the panel. I suppose this was aided by the fact that the gash was a bit irregular in shape, whereas the clean lines of the stich holes and panel gaps do make the fill color contrast a bit more noticeable.

I was also worried that the whiteish nature of the cellofil content would show through. However, as long as I carefully smoothed the fill and surrounding wood with a putty knife while wet, and sanded a bit when dry, things turned out pretty good. I didn't notice any discoloration in the wood surrounding the fill after the epoxy/glass application.

   Just like rjacobs said, I've found the cellofil and wood flour mix works pretty well.  Avoid getting much out onto surrounding wood, and use a good strong putty knife to remove as much excess as possible to limit sanding.  And then when the glue is hard, sand over everything down to clear wood surrounding the filled area.  If the filled area is just slightly darker than the surrounding wood, you've got the color right, as when the epoxy coat goes on the surrounding wood it gets darker, too. Most things will pretty much disappear by the time they are glassed over using this technique. 

I haven't tried it, but next time where I'm just filling stitch holes or little imperfections I think I'll test out a microspheres and wood flour mix, to make the sanding that much easier (even though sanding filled stitch holes is really easy relative to all other sanding on these boats).  For the slightly structural areas like your seams, I'd stick with cellofil/wood flour.