Thank you so much - My son took it apart I wasn't there and have been trying to figure out how they go back together - this all makes sense and Thank you!I'm not sure if it is a fitted piece of foam in the holes, but they do need to be sealed so water doesn't leak into the car. I usually put a thin layer of seam sealer on the backside of the hinge and then gob those square holes full of plumbers putty before putting the bolts in from the backside.
I look forward to the better answer that Leo will give when he gets time.
Man am I glad you posted this! It made me realize I forgot to seal mine when I installed and aligned my doors recently. What I do is, once I get the doors aligned where I want them, I take the bolts out and wrap the base of the threads with 3M butyl strip caulk and reinstall (one by one as to not lose the door alignment). Some of it squeezes out, which tells me they're all filled and sealed. Not sure what the factory used though.
