I don't know about gaskets, I've never taken my hatch off... Something that comes to mind for dealing with it is Eternabond. It is a tape used to seal RV roofs and the like. (Think duct tape but twice as thick and 100x as grippy/sticky.) You apply the Eternabond over the hole, then screw your bolt right through it - it will bond to the jeep and the bolt, making a water-tight seal. Worked on my RV roof when I re-attached my ladder, though those were smaller screws...
(TIP: clean the surface you are applying it to THOROUGHLY, and don't apply if it's too cold, say less than 60 deg or so. If it is cold, use a space heater to heat the area prior to application. The stuff sticks insanely well under the proper conditions, and only so-so when cold or dirty.)
Another options is some silicone around the bolt threads and head and then some of the spray-on sealant stuff like Rustoleum Rubber Coating from the top side.
BTW, I'm digging all the little details on your XJ (LED lights in bumper, split bench seat, etc)
And Congrats on the baby!!