I would think you would want to do two things:
1) Have the dome above the telescope on the overall view of the complex but set the transparency level so that the telescope clearly is visible through it.
2) Also have a dungeon map of the building level upon which the telescope stands and have that without the dome glass. Usually, when we do interior floor plans, we leave the roof away, so that one can see what's beneath it. The dome is nothing more than another type of roof. Therefore, it also would be absent on the floor plan, as opposed to the complex map. I'm referring here to your floor plan for the forth story or (European numbering) third floor.