Needed change: you must seal the outer edges of your hatch ribs and possibly the lower edge of your hatch -- they are exposed to weather. Even if or when covered by gasket or other materials.
One idea might be to notch the ribbing on the hatch to allow the hatch to close. Obviously more of an issue is there is a cross beam at the position of the counter. Or if the notch compromises the integrity of the ribs. No idea how much of a rib can be removed without failure. Could you brace the notch with metal ??
Two is to reduce the counter depth to allow the hatch to close. This might include rounding over the edge or cutting it at angle. Those draw saws might be able to make the cuts even if the counter cannot be moved. If the counter can be moved back, you would not be asking, right?
Two B is do both -- sharing the difference.
Three is to find 1 1/2" wide 1" thick gasket to fit along the entire edge of the hatch. Maybe a double door sill gasket?? Remember this gasket will experience high winds while driving. So any material will have to deal with the wind/exposure.
Your basic design -- the aluminum skin/T channel pressing down on a gasket seems to be a bit iffy. I know people do use it. However the design means that water/rain can be caught be the skin/channel and directed at the gasket-lid gap. The hatch could settle causing the skin to flex up, breaking or reducing the seal. The hatch could move up/warp also breaking the seal. The T channel is still susceptible to this issue.
A more common seal - an excellent drawing
http://tnttt.com/viewtopic.php?f=50&t=70278&p=1242303&hilit=hatch+seal#p1242303 uses both a gasket and the mechanical channel routing to slow/reduce water penetration. However using this design instead of your current design would most likely mean that the skin on the hatch and likely the sides would have to be adjusted along with changes to the edge ribs and possible interference with cabinets. Most likely a too late design idea.
