Thoughts on how to fix a depression in the roof

Not sure you have much to loose. You could push it up from inside. Sure looks like someone sat their butt on it.

You say it just appeared one day?

I doubt that Bondo delaminating from the substrate would do that. I would expect the opposite.
Yes. I noticed it after the car sat in the sun at a car show. I suppose someone "could" have dented it while I was wandering around the show but I highly doubt it.