The Stump Jumper is over engineered so I wouldn't worry about the damage.

Ditto on the Trek.

Take a file and remove a little of the metal off of the inside of the seat stay at the dropout for chain clearance. I've been doing that for years. Did it on all of the frames that I built back in the 70's, never saw a problem.

I had to file chain clearance on the seat stay when I put a 6 speed narrow freewheel on my 1971 Motobecane Grand Record. The chain would catch shifting off the 13T sprocket. The bottom picture shows how much of the stay I needed to file off for adequate clearance. That's not a particularly highly stressed point as most of the forces are going up into the seat stay rather then laterally loading plus there's adequate metal remaining. You can see in the vent hole how thick the tubing is at the bottom of the seat stay.