RT-38297 added support for INNER and OUTER strokes to NGRegion. Region code that takes care of rectangular borders still expects that INNER and OUTER strokes are rendered as CENTERED.
Sample code:

    @Override
    public void start(final Stage stage) throws Exception {

        StackPane pane = new StackPane();
        pane.setPadding(new Insets(10));

        StackPane child = new StackPane();
        child.setStyle("-fx-border-color:black;");

        pane.getChildren().add(child);

        stage.setScene(new Scene(pane, 300, 300));
        stage.show();
    }