A sunroof is a good culprit, but a few other options for water in the spare wheel well are; your rubber seals around the hatch itself could be pinched, it could be the diaphragms in the rear on each side, although a bit low down perhaps (these manage air pressure inside the car opening and closing doors), but the likely place is one of the hatch grommets. If there is a tear in the rubber from years of opening and weathering, water can go anywhere once onto the roof lining. Even a small tear will do it.
From unfortunate experience, much of the water volume runs down the D pillar and into the rear section and into the low point being the spare wheel well, that maybe the problem. You may also want to check any modules in the rear for water ingress, water can also sit inside near the wheel arches). Hatch itself may also get some.
hope that helps
R36 Wagon MY2010.5: Biscay Blue| Dynaudio and Nav| RVC| VW tow bar|
Mod highlights: ECU and DSG Tune| 3AA CCM and 7N0 Gateway| 3D colour MFD| MIB2 retrofit and 7N0 RVC| Quad LED tail, brake and indicator rings| Zimmermann Sportbrake rotors, composite pads| TPMS High| 2Q0 Blind Spot and RCTA| B8 rearview mirror|
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