The pictures of the nuts in your original post don't exhibit any corrosion whatsoever. I think that, if corrosion was the cause, they'd all be similarly afflicted.
Because the correct bolt torque is so low, I bet they were gorilla'd in, which started to strip the rivet nut in the roof rail frame. It probably would have been fine if left like this. When you backed them out, that rivet nut, which was probably already half spun in the frame, started to work the other way, which stripped it completely.
The accessory roof rails, I assume, are similar or identical to the OE roof rails -- just available in a box instead of on the option sheet. If the OE roof rails attach like the accessory ones, the dealer can order a new roof rail for that side of the van and swap it over in a matter of minutes. Or you could as well, if you didn't want this dealer touching the van anymore.
If you went that route, I wouldn't blame you. I started doing warranty repairs myself on our Town & Country, simply because I didn't want it at our local dealer.