To reproduce run the app and push the "Show lightwieght popup" button.
Popup will appear with a text field. It is impossible to edit the text field.


import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
import java.awt.event.ActionListener;
import java.util.concurrent.CountDownLatch;
import javafx.application.Platform;
import javafx.embed.swing.JFXPanel;
import javafx.scene.Scene;
import javafx.scene.control.TextField;
import javafx.scene.layout.HBox;
import javafx.scene.layout.VBox;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
import javax.swing.JFrame;
import javax.swing.JToggleButton;
import javax.swing.Popup;
import javax.swing.PopupFactory;
import javax.swing.SwingUtilities;

public class JFXPanelApp {

    public static String LIGHTWEIGHT_POPUP_BTN = "Show lightwieght popup";

    public static int SCENE_WIDTH = 200;
    public static int SCENE_HEIGHT = 200;

    protected Scene scene;
    Popup lightPopup = null;

    final JFXPanelApp.TransparentJFXPanel lightweight_popup_fx_panel = new JFXPanelApp.TransparentJFXPanel();

    public static void main(String[] args) {
        SwingUtilities.invokeLater(new Runnable() {
            @Override
            public void run() {
                new JFXPanelApp();
            }
        });
    }
    
    public JFXPanelApp() {
        final JFrame frame = new JFrame(this.getClass().getSimpleName());

        frame.getContentPane().setLayout(new BoxLayout(frame.getContentPane(), BoxLayout.PAGE_AXIS));
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

        lightweight_popup_fx_panel.setBorder(BorderFactory.createLineBorder(Color.black));

        final JToggleButton popup_button_light = new JToggleButton(LIGHTWEIGHT_POPUP_BTN);
        popup_button_light.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(java.awt.event.ActionEvent e) {
                if (lightPopup == null) {
                    Point location = frame.getContentPane().getLocationOnScreen();
                    lightPopup = PopupFactory.getSharedInstance().getPopup(popup_button_light, lightweight_popup_fx_panel, (int)location.getX(), (int)location.getY());
                    lightPopup.show();
                } else {
                    lightPopup.hide();
                    lightPopup = null;
                }
            }
        });


        final JFXPanelApp.TransparentJFXPanel scrollJavafxPanel = new JFXPanelApp.TransparentJFXPanel();
        scrollJavafxPanel.setBorder(BorderFactory.createLineBorder(Color.black));

        frame.getContentPane().add(popup_button_light, BoxLayout.X_AXIS);

        reset();

        frame.pack();
        frame.setLocationRelativeTo(null);
        frame.setVisible(true);
    }

    protected final void reset() {
        final CountDownLatch cl = new CountDownLatch(1);

        Platform.runLater(new Runnable() {
            @Override
            public void run() {
                lightweight_popup_fx_panel.setScene(createScene());
                cl.countDown();
            }

            protected Scene createScene() {
                final VBox pane = new VBox();
                pane.setMinSize(SCENE_WIDTH, SCENE_HEIGHT);
                pane.setMaxSize(SCENE_WIDTH, SCENE_HEIGHT);
                pane.setPrefSize(SCENE_WIDTH, SCENE_HEIGHT);
                Scene scene = new Scene(pane, SCENE_WIDTH, SCENE_HEIGHT);
                final TextField text_input = new TextField("TextInput");
                pane.getChildren().add(text_input);

                HBox button_box = new HBox(5);
                pane.getChildren().add(button_box);

                return scene;
            }
        });

        try {
            cl.await();
        } catch (Exception z) {
        }
    }

    class TransparentJFXPanel extends JFXPanel {
        float alpha = 1;

        public TransparentJFXPanel() {
            super();
            setOpaque(false);
        }

        public void setAlpha(float alpha) {
            this.alpha = alpha;
            this.repaint();
        }

        @Override
        public void paint(Graphics g) {
            Graphics2D g2 = (Graphics2D) g.create();
            g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha));
            super.paint(g2);
            g2.dispose();
        }
    }
}