Rock guard mounts separately, independent of window. So mount the window first. Then put down additional butyl tape and mount rock guard.
IMHO, it needs to be sealed, as it is attached to the same pieces of plywood that the window is attached to. So if water leaks
in, its going to rot out the same wood.
In my case, there were NO signs that there was ever anything under the rock guard framing. The window frames clearly had butyl tape under them. And I had by far the most rot on the front window plywood, more than the rest of the trailer combined.
If you have a gaucho model, then the top bunk is attached to the same window wood.
In the case of the Trillium
rock guard, it has a very similar aluminum frame that the guard attaches to, similar to the window framing.