The following code does not execute all the steps:

      try (WizardCommandController controller = uiTestHarness.createWizardController(JPASetupWizard.class,
               project.getRoot()))
      {
         controller.initialize();
         controller.execute();
      }

That is because controller.execute() does not call refreshFlow(). If controller.canExecute() is called before controller.execute(), then it works. The solution is to call refreshFlow() in the execute() method.