Controlling a Linux-based app from Windows

[CTorreno]

My testing project involves interacting with a Windows-based desktop app and a Linux-based application accessed via RealVNC. I can see that Au3Info can see the properties of the desktop app but when I hover over the Linux app viewer, all I see is the window title and none of the elements of the application being viewed.

Can I use AutoIT to create automated test cases where the steps jump between Windows applications and that Linux-based app? Furthermore, the Linux-based app is dynamic. It changes depending on what was clicked. 

Edited January 6 by CTorreno
added more info