I had minor a minor leaking issue with the rear hatch also (Alchemy S). I noticed that there were large spaces around the skeg control tube and there was also a hole at the top of the bulkhead that probably exists for pressure equalization issues.
Think of the problem this way; if you have a bottle with no holes and open the lid, water comes in slowly due to the pressure inside of the bottle. If the bottle has 2 holes water can enter rapidly as the pressure is allowed to leave via the secondary hole
I sealed around the skeg control with caulk and stuck a golf tee in the factory drilled pressure equalization hole. Leaks are no longer a major issue, not fully dry but not a major issue. (If I want to ensure a dry ride that is what I put in a dry bag).
I do not worry about losing a hatch lid due to pressure popping it off as it is under the straps in the J racks.
1 Canoe/Kayak Trailer
Sport Cases (Electronics)
Pull-Up Strap Handle Kit
Touring Kayak Paddles