Hm, a fun way around might be to do a sideview of the inside of the mountain instead of a top down. I can't find many examples but here's one done by Dyson Logos which shows a partly underground ruin as a side view of multiple layers.


He's also done another map I think might be inspiring for the question.


This is a village with a nearby dungeon which is underground, accessible by digging around in the pile of rubble shown, and there's a couple of examples of the tunnels overlapping in the top view to show that it's a multi-layer dungeon.

My solution to "it's partly underground" was to do multiple top-down slices which would reveal all of the layers.

And then the final module will hopefully also have a side view sketch to show that it's a tree hanging over a crevasse that you could go into and explore the root tunnels which have been dug out by the occupants.

Those are the only solutions I can imagine (overlapping, slicing, or side view). You might mix and match, do a top of the exterior city and a side view of the interior city (if it's tall and narrow) or do several slices with a key to explain the layers.