When I was at the factory back in 2016 for some service, they installed a gasket along the top of the complete compartment opening. It has what looks like a bunch of hairs on either side of a firm clear plastic wiper.
This is something that the door Mfg. suggested they do.
Hope that helps
Now this has stopped water from getting into this "side hinged" compartment door, but I still have a problems with the "top hinge" door leaking water at times, so much so, I keep a towel rolled up along the complete opening inside the help wick water away or keep it from flowing thru to the other side, which has happened. I really need to empty out the whole compartment and get someone inside and someone outside spraying w/ water and try to find out where its getting in.
2015 F350 DRW, 2015 Sequoia SQ38HRL, G614's, Titan Disk Brakes, Trail-Air Flex Air pin box, SRE4000 w/ X-brace, Heavy Duty Shackle Straps w/ Wet Bolts & New Springs.. Now I am done for awhile.