I found the line on how to do this in the intro doc.
If your graph structure is mostly tree-like, but you have a
few “extra” links that should be ignored for the purpose of deciding the tree
structure, you can set the Part.LayoutId attached property on those
links to be “None”.
There’s a more general way to do that, in case setting or data-binding that property isn’t practical. That is to customize how the layout creates its network consisting of vertexes (corresponding to Nodes) and edges (corresponding to Links).
So in your case you could construct your own TreeLayoutNetwork and have the TreeLayout work with that. But it sounds like you won’t need to do this.