Using modern materials, one way might be to use bathroom silicone sealant. loosely wrap the lid in cling film, put a bead of sealant round the lip of the deck hole, apply the wrapped lid firmly, come back a day later. Carefully remove the lid, remove the cling film from whatever it is now clinging to, you should now have a custom gasket.
Having a water deflector on the deck in front of the hatch will help. A clubmate had a Seawind - he spent a lot of time re-engineering his hatch. Kit yachts' hatches seem to attract a lot of attention. Maybe designers tend to be over-optimistic?
Looking at the pictures again. It will probably be better if the bowsie under the jib boom is let out about 1/2". This will then cause the boom to lie a few degrees off centre where it needs to be, an let the jib swivel line point at the top fitting on the mast. Also moves the fore sail a little further away from the mast, avoiding fouling and giving the slot between sail and mast that is needed for proper airflow.
The sail arm servo will benefit from better fixing. When it operates, all the force from the sails goes through it and its mount, and a twisting force is applied. At some point, the screw heads have to cope with this. One screw in each hole with a washer, or stainless larger head screws.