Also wanted to weigh in, it's definitely possible to do things through docking that can't be done in the editor. Another way to describe what happens in the editor is that you can have multiple branches off of a part but they can't all reconnect later. For instance if you use a three way coupler (tri-coupler? I forget) to branch down into three parts and then try to attach an inverted tri-coupler, only one connection will be sound. The craft format can't describe a situation where all three children merge back into one; only one path can continue and the others have to terminate. Making it structurally unsound and in need of strutting. But the format is different in the persistence files. (the save files). From what I can interpret of it, it doesn't depend on a root or parent/child system.