Yes, the window Z-order can be set using:
WindowProperties.setZOrder(WindowProperties.Z_top)
See also this topic for a discussion about that.
Actually, I once requested a feature that would keep a secondary window always above a primary window, so it would never get lost below other, non-related windows. It might still be on the devs’ todo-list. Here is the relevant post.
And yeah, whether we like it or not, window managers decide what to do with the window(s) of our application, not the other way around.