No, no dust can get on the coins once they are sealed in the pliofilm. Before packaging ? Yeah, dust could get on the coins before they were packaged, but it would get on all of them, not just select coins. And in point of fact there are plenty of sets from that entire time period where you can actually see dust on the coins - inside the packaging. But I've never known it to cause toning per se. Spotting yes, sometimes, but not general toning.
I have a Franklin that I removed from a PF set with almost the same tones. But every other coin also was toned in the set. The Jefferson is a dark green.
As Doug said, the plastic is air permeable. Now lay the set flat, and put something flat on top of it. The envelope is going to be pressed up against which coin more than any other? Te half dollar because it is the thickest. So if any sulfur migrates from the envelope through the pliofilm, it is most likely going to get to the half dollar.
I have an early 60's proof set that really toned while setting in a box for years. Can't remember when the last time I had looked at it. At least 40 yrs ago. I'll have to dig it out and snap some pics.