A general question about Windows behavior and AOT

Anyone ever notice when using another machine like a VM or TS session in fullscreen that it makes Always On Top behave weird? (And this is not just limited to Xion -- I notice it in all programs that use AOT, including the Taskbar) I suppose what's really weird is that it doesn't seem predictable -- sometimes it works, sometimes it doesn't. Even when it's on a separate monitor, it still affects the AOT on other screens.
Just curious what exactly it is that is controlling this behavior.
Just curious what exactly it is that is controlling this behavior.