The rule of thumb is "epoxy sticks to everything, nothing sticks to epoxy". So regardless whether you put a skim coat on it or paint it, you'll need to rough up the surface with 80 grit or coarser to get it to stick.
Personally, I would just hit it with some 80 grit and prime it. Why spend the time and money to pretty up the inside of the transom?
For future reference, if you roll peel ply (also available from US Composites) into the surface of the layup before the resin kicks, then peel it off after it has cured, it will leave a surface with sufficient mechanical keying that you don't need to sand before applying paint or more laminate.
BTW, I think your layup schedule is spot on. Your laminate thickness is probably 1/4" or so and your transom will be solid as a rock.
Dave
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Blue Heron Boat Works
Reinventing the wheel, one spoke at a time.
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