I noticed the same on my 2016 R estate about a year ago. Put some grease on it and forgot about it until a couple of weeks ago when I noticed the same rusty water marks. The door was also not holding well in the fully open or half open positions.
I took the check strap out and the rubber cover off and it was full of rust. Both of the springs inside had disintegrated so water must have been getting in. The seal that is visible was dirty, but in good shape, as was the seal end of the rubber cover inside the door.
I think the check strap was replaced before I owned the car, and the cover wasn’t put on properly. Or possibly the cover has been moved by the window mechanism retracting inside the door, enough to start letting water in.
I replaced the check strap which was about £25 from the dealer. The hardest part of the job is drilling the speaker rivets out to access the inside of the door. I put it back in with threaded rivets incase i need to get in there again.
From the the rust marks in your pictures, I’d say its likely to look like mine on the inside.