The only thing that can go on top of an always on top application is another always on top application, and even then, an app can tell if it's on top or not and may have been coded to fight for the top position.
This is something that is specifically coded for the app and can't normally be fixed, at least not without hacking at the application itself (Possibly while running).
I did find this which seems to do just that:
Download Always On Top Maker 1.00 Free - Always On Top Maker - a tiny tool to make a window "always on top (TOPMOST)" - Softpedia
It says "always on top maker" but it also does the reverse. Though I have not tried using it and can't say how well it works or if it might not wreck the program and require you to reinstall it. So I'm not endorsing it either way