Jschoef: there are 4 bump stops that support the hatch when closed. If the upper 2 bump stops (midway up the side of the hatch) are extended out too far, they'll prevent the lower bump stops from contacting.
There are several threads about adjusting the bump stops. Maybe this one will help:
My similar rattle was related to some cables, I believe the ones which connect to the rear seat fold release. It was fixed after my 3rd SC visit. Vin 058###.
teslamotorsclub.com
Adjusting the stops inward might correct your water leaking. However, if the hatch isn't supported evenly/correctly, it will pulse (buffet?) while driving over rough pavement, creating some uncomfortable ear issues.
Hope this helps.