[Autobahn_Burner]

I would say, the solution is simple but strange. It is the tailgate because it is leaking by design: water enters around the rear handle area (below lic plate) and gathers at the bottom of tail gate. Once one opens the tailgate after rain, water is running from bottom to top of the interior trim panel of tailgate - and from there it poures rear hatch area, from where is drops directly into the jack compartment. It took me months to get it.
Solution: remove the three rubber grommets at bottom of tailgate. Excessive water will exit the tailgate instantly.