Regarding those roof trim strips that were removed. I can't be sure but I guess there could be a hole that rusted underneath it in the channel. However, if a hole had rusted in that channel I would think the car would display some significant areas of visible rust elsewhere. I've never pulled the channels on my car so I can't say what it could look like under them. A quick search on-line seems to indicate those channels are kind of a basic item that is held in place with pieces of 3M adhesive pads or something similar. I wouldn't go pulling those channels out to see what may be going on under them until you clean up and seal those gaskets with a bead of Green Grease and see if that fixes the problem. Here's the first thing that popped up when I searched that roof channel...

https://truelineautomotive.com/produ...gle%20Shopping