If we run below test program, background is filled with black color.

import javafx.application.*;
import javafx.scene.*;
import javafx.scene.control.*;
import javafx.scene.layout.*;
import javafx.scene.paint.*;
import javafx.stage.*;

public class TestUnifiedStage extends Application {

    @Override
    public void start(Stage primaryStage) throws Exception{
        boolean allowsUnified = Platform.isSupported(ConditionalFeature.UNIFIED_WINDOW);
        System.err.println("Unified windows " + (allowsUnified ? "ARE" : "are NOT") + " supported");
        primaryStage.setTitle("Hello World");
        primaryStage.initStyle(StageStyle.UNIFIED);
        final VBox vBox = new VBox();
        //vBox.setAlignment(Pos.CENTER);
        vBox.setStyle("-fx-background-color: transparent");
        vBox.getChildren().add(new Label("Hello World"));
        
        // remove this and it works!
        primaryStage.setScene(new Scene(vBox, Color.TRANSPARENT));
        primaryStage.show();
    }


    public static void main(String[] args) {
        launch(args);
    }
}

Looks like the issue identified in JDK-8095040 has resurfaced. Issue can be seen in JFX25 and i have also checked that issue happens in JFX21.
If we run the same program in 8u431 it draws properly.