Say you put a CheckBox within a VBox and set a margin on it. The FXML written will contain:

        <VBox>
            <children>
                <CheckBox mnemonicParsing="false" text="CheckBox">
                    <VBox.margin>
                        <Insets bottom="3.0" left="3.0" right="3.0" top="3.0" />
                    </VBox.margin>
                </CheckBox>
            </children>
        </VBox>

Now if you move the CheckBox out of the VBox, or wrap it in an HBox, or take any action which results in the CheckBox no longer directly enclosed within the VBox then the <VBOX.margin>[...]</VBox.margin> will remain but is no longer editable by SceneBuilder. What about cleaning it ?

I agree that if an FXML file contains such a construct at load time then we must preserve it.