I'm not familiar with the Mki, but on my Mkii at least, there is no weatherstripping, there is a channel/gutter all the way around the opening that the top hatch fits into. If you're getting rainwater in, I would suspect either the gutter is clogged or the hinges are leaking. For the hinges, I would re-bed those with some butyl tape. Or maybe your gutters have sprung a leak? My hatches are hinged to open forward so it's pretty easy to inspect the gutter.
I also have things like the shower handle and speakers back there that are potential leakers.
Good Luck
Rob.