The floating Pane is placed inside a ToolWindow which Owner is the Docking and that is why it is always on the top of the MainWindow. So in order to achieve the desired behavior we should remove its Owner. The easiest way to achieve that is to create a custom ToolWindow which inherits from ToolWindow and override its GetWindowOwner method to always return null. After that through a custom GeneratedItemsFactory you can pass the custom ToolWindow which doesn't have Owner. For your convenience we have prepared and attached a sample project which demonstrates the exact approach.
Hope this helps.
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