I have had the same issue with one of my compartment doors since I purchased my 2017. Short answer is, no. I haven't found a way to completely eliminate the leak around the door. Mine comes in around the door seal itself, only when it rains in certain directions.
The best solution I've found is to adjust the lock mechanism and secondary latch to put as much pressure on the door as possible when closed. The added pressure seems to help keep the water intrusion to a minimum.
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2017 Jay Feather 7 22BHM Baja/Andersen WD
2018 F150 4x4 3.5L Ecoboost Max Tow
2015 MB Sprinter 2500 Passenger 2.1L Diesel
2007 Ram 2500 4x4 Cummins 5.9L G56
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