Are there any gaps around the skybox brush? If it's flush against the windowframe and window, then it should work
Maybe you could make an outside aesthetic that makes it look like a building, like a stone wall with some pipes and wall trim? It would be kinda weird if you couldn't see it.
The offending wall is in PVS. As such, it is rendered. What you need to do here is to put another wall in the way to cover up the first one. In short, you will have to model part of the outside in the real map, not in the 3d skybox.