I have the same problem. Once I enable BiDi, modal dialogs don't appear anymore.

    ChromeOptions options = new ChromeOptions();
    //options.enableBiDi(); // uncomment this line to reproduce the error
    ChromeDriver driver = new ChromeDriver(options);
    driver.get("https://the-internet.herokuapp.com/javascript_alerts");
    driver.findElement(By.cssSelector("[onclick='jsAlert()']")).click();

    // throws "no such alert" if BiDi is enabled:
    Alert alert = driver.switchTo().alert();
    assertThat(alert.getText()).isEqualTo("I am a JS Alert");