@Crimson Horizons
Interesting points. I certainly like the idea of it being possible for the rules to cope with subterranean domains, and I think that you might actually have largely answered your own question in your explanation of your concerns.
If an underground development would receive the benefits of certain above-ground ones, then include the costs of those things in what you charge for setting up the new subterranean zone. I.e. if you give the benefit of City Walls to every underground settlement, then preparing a city district site would entail the cost of 4 sets of city walls (32BP) in addition to whatever you charged for opening up the space itself.
That kind of expense would certainly limit expansion to a slow crawl for any underground race, and would strongly encourage heavy development of an existing settlement before any expansion was considered - which would in turn seem to fit the politics and settlement patterns of Golarion.
You'd need to figure out how to handle the costs of 'claiming' a hex, and whether you wanted to tweak the expense associated with clearing different terrain types - hills and mountains should arguably be easier to develop underground dwellings in, with forests and plains tough, and swamps nearly (or entirely) impossible.
Roads, unless they're run above-ground, are presumably going to be more expensive to develop since they involve massive amounts of digging: perhaps a base of 8BP (double the cost of the most expensive conventional road networks).
Likewise, I'd recommend tweaking some other effects: a network of caves, for example, wouldn't merely be a 'safe refuge' granting a minor Stability bonus to the realm, but would be a huge cost-saving on setting up a settelement - at the least I'd go with the Kingmaker-standard halving of cost for relevant work (in this case, the opening up of city districts) instead of the Stability boost. If nothing else, this'll strongly encourage underground races to concentrate in places where caves are to be found.
Even claiming a hex is likely to be different - after all, to +do+ anything with it, space has to be opened up. I might let subterranean kingdoms 'claim' as much land as they like - but until they dig roads through it or open it up for other uses, it gives them nothing at all in the way of either cost or benefit: it's just a load of rock over which they have no power at all.
It'd probably make sense for a hex with caves (or ruins, to allow for those famous monster-haunted castles and lost cities beloved of fantasy gaming?) to be claimed and settled without much expense... but it's hard to think of anything else that could be easily moved into by races that want to have stone on all sides.
And for any development you're again looking at a lot of digging. E.g. I'd guess that subterranean farms would cost at least 16BP to develop (eight times the cost of a hex of surface hill farms, but still much less than opening up a defensible city).
Overall, these kind of figures would leave most humanoid tribes lurking in undeveloped caves and / or ruins, with only a handful able to get together the funds required to found any kind of a capital. But with good leaders and a lot of hard work - or generous allies throwing resources their way to get things going - they might manage to make something of themselves.