Any panels/parts removed for mods? Are the rubber plugs just behind the roof, under the hatch in place and in good condition? Have you removed the side roof covers to check for intrusion routes?
FYI, water intrusion on a new vehicle rarely happens while driving in the rain. Angularity is wrong and rain is shed too quickly. Even car washes are probably too brief. It is usually a small gap that only shows itself with a large volume of water over an extended period of time. My dad ran a sprinkler on his SUV for two hours then drove his new swimming pool to the dealer. Got a new vehicle out of it.
Also check for a urine smell. If you're scaring your passengers they may not want to admit to pissing themselves.
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