I would find some weather stripping that is high density foam or neoprene preferable with a sticky backing and apply it to the underside of the hatch flange keeping it about 1/4 inch from the edge.
Now position the hatch where it should be and mask the deck around it with tape/ Remove the hatch and apply masking tape to the topside edge right up to the border.
Apply a decent bead of black silicon RTV to the edge on the underside of the hatch flange. Carefully position the hatch but don't press it too hard. Add some sealant to the screw holes, clear is probably better than the black but the RTV can be used if you are careful not to make a mess. Screw down the hatch securely but not super tight yet. Smoothen the outer edge and RTV squeeze out with your finger. After a minute or two or three, carefully remove the masking tape. Wait another hour or so and retighten the hatch screws. Be careful not to squeeze out all the RTV. You just want make sure the rim is well seated and sealed. It will take several hours to overnight for the RTV to cure. When it is cured it will have formed a silicon gasket under the flange.