I'm sorry, like PowerPoint, GoToAssist assumes you are working with the live session when you move into full screen mode. The alternative would be to drag the window frame as large as possible without selecting 'maximize' or similar.
I will alter this posting to an 'Idea' for other Community member to weigh in on.
IMO, always on top should be an option. If it gets hidden by another application, I can just click the icon in the task bar like I do with every other program. Frequently I have to minimize it, then move the program to another monitor because something opened behind it.