I think the blotches are either amine blush or (more likely) abrasion marks from either a covering or handling. Giving the boat a good scrub with plain water and a scotchbrite should mean there is no blush left, and a swift rub down with about 220 sandpaper should mean the epoxy is perfect for varnishing (or if you're a perfectionist, go to 400 wet sanding)

Once you start using the boat, you will pick up a few more blemishes anyway, and nobody will ever notice them.