Ashley before I go and make a bug report I figured I better get a better understanding of how exactly the mesh feature is supposed to interact with collision polygons.
My understanding is that the polygon should contort to match what the mesh deform does, within reason. Obviously overlapping, and odd angles might not work.
If you take a look at this project:
dropbox.com/s/wv44tu2wlncftam/polypointsmeshbug.c3p
You see that just setting the mesh changes the polygon, and even looses a point.
Then if you try to move the mesh the collision polygon just distorts to cover the top, but places all the points at the top of the mesh. Leaving only the top of the object usable for collisions.