This is not strictly a GSX support question, since the position of top message bar is controlled entirely by the sim, even if we can control the display time for each message.
However, if multiple different apps will print something to it, messages might overlap each other, which is also a reason why we try to not display it for longer than it's necessary.
Your comment about the message bar being blocked by the P3D menu is strange though, since by default, its position should be right below it. That seems to indicate you, or another application, has moved it somehow, since like any other window, it can be undocked and repositioned.
The only thing sure, we don't do anything like that from GSX.
