Since virtually every window in the UI now uses the current frame nesting, its unlikely they will change it in a way that requires every window to have the same change.
However, they could easily implement some function that fires on close button press that wont be triggered if you close the window via script.
For example, there does seam to be some function call to save setting changes when manually moving windows or using the settings window that isn't triggered if you move a window via script.
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