I'd use a sanding block and knock down the rough edges that are apt to snag something or slice your hand.  As you say, no one is going to see it so do not worry about the looks.

Paul

What Paul said. That's what I've done on three boats. Use a very course sandpaper and it will take only a few minutes. -Wes

I used my paint scraper (I think works better than sandpaper on long raised linear features like this) to reach as far as I could to knock down those raised edges soon after it had cured so it wasn't rock hard.  I was concerned this might have gone through the epoxy into the glass, so I then put a thin coat of epoxy over the edge then next time I had a batch mixed up for some other purpose.  This also helped to smooth things over.  

Kathy

You should at the very least hit the rough spots to prevent poking holes in your dry bags or snaging stuff. On the other end of the scale you could give it a nice finish. It's really up to you...

Thanks everyone.  I'll just sand down the edges.  Dehager - That looks amazing.  I'd love to acheive that finish, but it would extremely difficult in the shearwater, which uses a taped seam at the hull-to-deck joint, rather than shear clamps.  If I had five-foot long gumby arms with eyes on my hands, I'd give it a try.  Given my limitations though, I'll just try to keep the hatches on the boat when showing it off.

 -Zach