Okay, I did the change, now when you select a structural object and one or more axes systems, and press the Structure button (like before), the resulting object is now a separate "StructuralSystem" object. The only difference, actually, is that both (the original structure and the structural system) can have their own set of additions/subtractions, so you have complete control over what must be added/subtracted and when.
git commit 08d2121