What are the known areas for water ingress to the side wells and spare tire area? PO did a poor job repairing the right rear quarter panel and spare tire floor so will need to be done again.
1. Liftgate seals?
2. Liftgate hinge bolts?
3. Tailgate hinge bolts?
4. ??

Bumper attachment bolts also leak which was the main leak area for me leading to an inch or so of water in the spare wheel well causing the air compressor to misread the temperature.
I sealed the bolts up when installing a factory tow bar as they had to come out anyway, there is a foam type gasket that sandwiches in there, not sure how waterproof it is because it doesn't look it.
I also replaced the main boot hatch rubber seal as a precaution. It's been fine since and bone dry although I have also removed the drain bung in the base of wheel well to prevent any build up in future...just means can't go wading too deep.

Thanks. I remember reading about your leak. Somehow confused liftgate bolts with bumper bolts.
Have I read that the side windows can leak too?

I have heard that too and the 'official' fix was a factory plastic water shed that went over the top of the Nav unit. Not sure how that was a fix, it was just avoiding having to do a proper fix!

If where it's leaking in is not obvious you can try putting some tissue paper around suspect areas and leaving it to see where it gets damp. The bumper bolts where obvious on mine as there where drips of water on the ends of them.

I did the hatch seal as it was past it's best and looked suspect in a few areas, think it was £90.