Tracking Issue.
As to populate the, quite frankly, sparse underground, some small dungeons scattered around Gaia may make for some variety. These range from small dungeons like the Overworld, to larger side-questing dungeons. To entice players to these structures, add some features that can only be found here.

Loot: Various assortment of gemstones. Some foodstuffs for resources. Random items to stock up on, like Sticks. Rarely, some tools.

Mobs: Perhaps add some mobs that can only spawn in certain underground structures, alongside other mobs that only spawn in dark caves.

Dungeons: These vary in size, and are made up of Gaia Stone Bricks and other types of Gaia Stone. Layout of these dungeons may need some consideration.

As a side note for Loot, should the player explore various dungeons to find a key that can be used to unlock the first boss structure?

In all honesty, the underground isn't that sparse anymore, thanks to having cave gen (as this was written, caves did not generate). Perhaps this should be reduced down to maybe 1 or 2 mini structures, and have some overground aesthetic features.

Still, not quite sure on what to place underground.

I'll move this into planning than implementing into 1.0. It can wait