If you are just filling the holes and then putting a stretchable EPDM paint on over it I do not think the Bondo will come loose especially if you push it into the holes.
If you were going to try the bondo on the whole area and the roof flexed then it may pop loose over time. I am not sure about a large area coverage and a flexible metal roof. Ask some auto body shop about the Bondo for body repair. The Bondo for metal may be just enough different from the All Purpose Bondo that it adheres better.
I use the All Purpose on seams and to fix wood damage. My roof is wood covered in EPDM with metal around the edge and vents, etc.. I have used the Bondo with good results on the metal and to bond wood to wood and wood to metal. The bondo on my repairs has been good for a long time. One painted wood/bondo support has held up to years of exposure in my back yard.