How to open and render in a second window with OpenGL / JOGL with NEWT
So after letting this lie for quite a while, I just came back to it. Turns out, the error was in my code with a faulty false return value which would lead to a System.exit. I have no idea how I didn't catch this the last time round, but it now works with Try 2. That is:

public class SubWindow implements GLEventListener
{
    GLWindow glWindow;
    Program m_program;

    public void createSubWindow(int windowWidth, int windowHeight, boolean isFullscreen, String windowTitle
            , Program program)
    {
        GLCapabilities caps = new GLCapabilities(GLProfile.get(GLProfile.GL3));
        caps.setBackgroundOpaque(false);
        glWindow = GLWindow.create(caps);

        glWindow.setTitle(windowTitle);
        glWindow.setSize(windowWidth, windowHeight);
        glWindow.setUndecorated(false);
        glWindow.setPointerVisible(true);
        glWindow.setVisible(true);

        m_program = program;
        glWindow.addGLEventListener(this);
        glWindow.addKeyListener(m_program);
        glWindow.addMouseListener(m_program);

        Animator animator = new Animator();
        animator.add(glWindow);
        animator.start();
    }


Where the Program is one of my own classes handling the logic and the SubWindow class additionally implements the required init, display, etc. methods.