I have the same problem, and I can also see rust traces around the spot welded joint under the trim on the rear C pillar.
I looked at the rear quarter light seals, but there is no evidence of water ingress there.
I am going to strip the boot trim out and try the watering can, starting at the bottom and working up.
If you find the leak, do not use silicone, try Sikaflex or Wickes Ultimate Sealant instead, dont worry about the 'forget nails' title, these sealants are polyeurathane, the are flexible for 30 years, you can wipe any excess off with white spirit, and you can paint them.
I used to assemble the black detachable roof for the Frontera, and that was the only sealant the Japanese would accept on quality control.