As I have a hero hitting with a sword on one side and there for having one side alpha larger in the image than the other,
to have space for the sword down.
I had to realize that the new custom collision shape does not flip (horizontally in this case) with the graphic if this behaviour is used.
A way to avoid this is having the hero centered in the image but this would also require the same amount of alpha on both sides which creates a very wide asset.
The expected behaviour would be to flip the Collision Shape with the graphic, so the graphic doesn't have to be perfectly symmetric to be used with the "flip graphic" behavior.