I did the roof rack delete on my 2013 Trail cuz the cross bars rubbed on the lintel of the garage, bit better mpg, and it just looked sleek as sh!t. Then I had to clean up the work room where I was storing the rack and my son said it was easier to find the 4Runner with that unique rack on top, so I put it back on. Now the driver's side seat belt gets wet when it rains. Will admit I didn't do the best of jobs of cleaning the threads, was in a hurry.
Just waiting for a warm weekend when the missus or kids don't have me busy, and I am going to monkey with the screws, Loctite and or RTV to try to seal the threads; needs to be warm for it to cure. Not sure if I should chase the threads with a metric die and risk removing the black oxide. PITA clearing that crap out. Might just buy new bolts.
Point is, you might have a leak there. Just search roof rack delete and you will see the holes near the B pillar.
Small edits.