G'day Tor,
I did a flush hatch on the rear deck of my Laker and used a rubber seal. The hatch is held on by concealed bungees and so far has worked well
The pics below tell most of the story but a few words of explanation are warranted for a couple of items.
First is the type of rubber for the seal needs to be very soft as the hatch is being pushed down over a relatively large area and it needs to distort the rubber to effect a seal. I tried harder ones but they would not seal - although they might work if the woodwork is absolutely perfect.
Second is that to help the seal I created a thin ridge on the underside of the hatch by epoxying a thin nylon cord (similar to brickies line) in a line just in from the edge all the way around. This was given several coats of epoxy to completely saturate and then build it up a bit. It seems to do what was intended as it leaves a ridge in the rubber.
Lastly in order to make the hatch truly flush there must be a positive stop for it to rest on. The top of this stop must be level with the underside of the surrounding deck with the rubber seal sitting slightly proud of it. The idea is that the hatch compresses the rubber until the stop is reached. You can see how mine is arranged in at least one of the pics but it is not overly clear. To make room for the seal and stop you need to insert a spacer of the same thickness as the stop material between the deck and the supporting frame that the seal and stop sit on.
The words above may be somewhat confusing - this is definitely where a picture helps. Anyway have a look below and see what you think. If more explanation is needed I will do a cross section diagram of the system.
Hope it all goes well.