Fill them (see note) with a good filler or 'glass & resin, leave a dimple for gel coat or plan to drill down an 1/8", then mix up gel coat and "paint" the gel coat in/on with a good quality artist's brush. Take your time and don't make it worse by trying to make it perfect.
Keep in mind you don't want to create extra work down the road when it comes to a full finish.
Note: I would mask the area by taping over the holes and surrounding area. I would then cut through the tape just around the holes to be repaired.
An option for the holes on the top of the transom would be to mount a cutting board on top.
An option for the holes on vertical planes is to mount tool holders, pole holdes, rod holders, etc.
Personally, I would go with filling the holes.