The three locations in my photo are the ones Rhino Rack expects you to use.
See this page,
TOYOTA LandCruiser 200 Series 5dr 4WD 07 to 21 | Roof Racks & Accessories | Rhino-Rack AU - https://www.rhinorack.com/en-au/fit-my-car/results/594/toyota-land-cruiser-200-series-4dr-4wd-11-07-on, specifically these images:
The very front mounting point that you're referring to, in front of/over the sunroof, seems to be quite a bit lower than the other ones, and I suspect that if you install the Rhino Rack mounting pads, feet and cross bar there, it won't sit level with the other cross bars. You might also get more wind noise and/or sunroof interference.
Water ingress won't be affected by the locations you use, as the pads themselves don't provide any waterproofing - that's done by whatever sealant you use around the mounting bolt holes.