It is a good question. I have had the same experience of working in a desktop sharing session and then finding the main UI has logged out.
The user activity timeout is a system wide parameter. A change in the time can be requested by opening a ticket with support.
We actually do some tricks to keep the child window containing the remote access applet from timing out during a session. So this is separate from the user activity timeout.
It seems the only solution is to request a longer timeout if you don't mind also making the same change for all users.