The upper limit depends on what you're looking at! In the case of an encircling wall, a forest or another structure that doesn't completely cover the area, it's the echo boundaries. In the case of say, a mountain, which could "grow" from under the houses of the cities the upper limit is also the echo boundaries. In the case of things that cover their area like for example Hogwarts, the upper limit is the free space that is available without (too many) houses being crushed for it. There are no limits to how high a structure can be.

Concerning things within other structures: As long as they are landmarks in themselves and can exist without the surrounding parts of the building/castle/mountain, they are also eligible for this! Say, if someone built a house inside a mountain, both the house by itself and the mountain including the house would be possible echoes in this specific instance.