Currently, the theme css (Preview > JavaFX Theme) are set as author css instead of user-agent css.
To show a correct view to the user, the CSS Panel has a workaround in place that moves these theme css from author (Stylesheets column) to user-agent (Defaults column).

Once the user scene graph will be put in a SubScene, we'll have to remove this workaround, since the theme css will be set as user-agent css on the SubScene.