For things like that, they could build special versions of the star ship which remain in orbit as the housing. They would need no flaps, no tiles, just the 6 engines and the fuel tank. The body of the starship itself would be the telescopes tube.

You could do that, you could also use it to transport pieces of massive telescope arrays that self assemble in space.

Sure, thats what they did with the JWST. But that ist complex and expensive. A custom Starship could be the cheapest way to get telescopes up to 9m mirror size into space as you can assemble everything on the ground and you don't need a separate housing.