When i ungroup the resulting Object and then name each object, I'm able to run a simple Marionette Network that sucessfully adds and subtracts as the second object in the plan shows.
I made the Marionette today with VW2016 SP2 R1 (Build 288897) (German Version)
I think the weird behaviour of the Polygon is because the Get Bounding Box is behaving differently in a 2D or in a 3D view. Yet the calculation of the coordinates seem to be reliable. So I could simply delete the weird Polygon in the end.
Here is another version of the Marionette that doesn't act that weird
(sorry for my bad english)