While I find the idea interesting, I have to agree that your implementation is missing a little something for my taste.
First: there's no reason that a fully developed city would need to be on a planet that is 80 % hab for all your citizens.
We already have the technology to change the habitability of individual buildings (skyscrapers need to be climate controlled because the uppermost stories would otherwise be quite uncomfortable to live in, we have laboratories that have very controlled atmospheric compositions to prevent certain types of matter from reacting, we have submarines and planes for high altitutes that are regulated, etc tt), so a space faring race should not be depending on the planets natural habitability for its citizens on a planet that is as densely industrialised as the vision you described. You'd have districts and tunnels that would allow citizens that cannot naturally survive on the surface to get around in comfort and safety, with airlocks and rental suits at any exit that leads into an environment that would be harmful for the occupant.
This is also important because otherwise, multi-cultural empires could only construct such a planet on Gaia planets, which is a bit limiting.
Second: the proposed planet needs to be at least no worse than a normal planet or a ring world, because otherwise why build it rather than using the system for a ring world instead? Currently it seems to come with a whole lot of restrictions and debuffs (I know, industrial and other layers give buffs, too, but they don't sound as if they really make up for the increased costs).
I'd propose something along the line of GROWING such a planet to become useful. There should only be the one - it would be a massive undertaking to build, sustain and find a use for such a planet at the stage of civilisation we find out game start in (such planets are usually staples in universes that had advanced civs interacting for thousands of years over thousands of planets, it's a bit unlikely that we would even have one only 100 to 500 years in with a measly few hundred lightly populated planets).
Being inefficient at the start is fine, as long as the final product is worth the investment. Something along the line of covering the entire planet in farms as a first step - that would pay nothing, serving only to serve as a base to feed the many, many people you expect to house. This is on the surface and the first level because it A just makes sense that you'd need the food to sustain your population first, and B because it is much easier to just use the existing planetary atmosphere to aid in food production where possible than it would be to create regulated underground farms for the same purpose. (for roleplaying, just pretend that some of those farms are still cimate controlled to allow for the production of food for species that would not thrive in this environment, if any are in your empire)
Once the surface is filled completely with farms of the highest level (I'd envision this as end-game tech, further even than ring worlds because it would allow one planet to house several planets worth of pops, rather than eating an entire solar system of celestial bodies for the same purpose), you'd have the opportunity to upgrade your planetary HQ into one of three kinds: science, unity or industrial. The planet would have a permanent bonus to energy credit production no matter which type you choose, owing to the idea that a planet filled with tens to hundreds of billions of people would produce the tax income expected of such multitudes (for tax examples, take the amount of money someone in inner-city New York is expected to earn and the expenses he or she would be expected to bear - the planet is basically a huge, incredibly densely populated mega city and living there would probably not be cheap).
Choosing the type of production you want will then let you build your first producing section. The section would have the same amount of tiles as the original surface of the planet (making 25 tile planets intensely attractive for this project) and would cost something akin to 100, maybe 200 minerals per tile. Those costs represent the effort and materials needed to excavate the entire surface of the planet, reinforce the foundations of the buildings above, connect the surface with the deeper layer in a sensible manner and properly cable/connect internet/utilities and just generally try to plan for the future transit of several deeper levels through this one.
This level could have a small bonus for the production of whichever resource you chose when you upgraded the HQ, but it shouldn't be more than 5 to 10 % - a boon, but not a massive one.
Once you construct the 3d level (costs for this should rise by 10 to 20 % per tile, you excavate even deeper, stuff needs to be funneled up through two levels and gotten rid off if your industry has no use for it), you get the opportunity to build the second unique building for this type of planet (first was the HQ), a type of built-in planetary space port. This is both useful and necessary because it allows freighters, haulers and transport liners with atmospheric capabilities to land on any of the existing or future levels of the planet to trade, pick up stuff, deliver ores or whatever else the planet may need (I'd envision unity production to be about having a centre of spirituality/schools/monasteries what have you on the planet, which would need people to be able to visit to be effective).
This building would replace 1 building on each layer of your planet, serving as a huge access hatch/elevator bank and would add a small planet wide modifier to whatever resource you selected (+ 5 %, pushing the second layer to 10 or 15 % + whatever modifiers you have access to and + the pop modifiers - we're getting somewhere).
The fourth layer would become yet more expensive (the first was between 10 to 20 % more expensive to build, this one would double that). It would not introduce a new building, but would introduce a further buff: tapping the planetary core, a small bonus to energy credit production generated by using the heat and pressure of the planetary core to cheaply power any appliance all the way up to the surface. This layer might also have a small, layer-wide bonus to energy credit production for the same reason, if that seems necessary.
The fifth and final layer would consist only of a command & control building in the centre of a 9 tile square, be roughly double as expensive to build (in total) as the first layer and come with the opportunity to build a total of 8 unique buildings.
Two of them could serve security (with one pulling double duty for espionage, if that ever becomes a thing): a planetary security agency to reduce unrest and fight crime (think FBI or elite future cops to ferret out crime in a city the size of several planetary surfaces) that gives boni to unrest reduction and a small happiness /ethics diversion buff via keeping the peace and a permanent military garrison (massive buffs to defensive armies stationed on the planet to make your humunguous planet harder to take - if possible, it should negate much of the reduction in efficiency that comes with bombing, as it serves as a deep reserve for military forces that is 4 layers under the surface and hardened against bombing/siege).
The rest would be administrative buildings that convey a tiny but empire wide and stacking bonus to a resource of your choice. Something like the galactic stock exchange, but smaller and repeatable only on this planetary type and layer. You could build 8 empire tax and custom hubs that boost production of energy credits by 1.5 % each, for example, or just go for a more balanced spread of 4/4 in energy and minerals or 3/3 with the two security buildings.
If we ever get even larger maps and if the gameplay gets extended further out, you could introduce a tech that allows you to have more of these planets or unique ethos buildings that are only producable on this planetary type and the lowest planet layer and that boost an aspect that would benefit that ethic.
As capital planets never join factions, you could make this planet your capitol and as such assure a heavily fortified, hugely productive planet that gives empire wide buffs as the centre of your empire.
For the reason that this would be a very expensive and tasty looking war target, the system would probably both heavily defended by stations and should have a mandatory full garrison of your most bloodthirsty troops + a planetary shield generator.
It should only be selectable as a war target under the condition that you need to ACTUALLY TAKE IT, because otherwise making it resistant to invasion would be pointless, and it should come with a price tag between 3 and 7 times as high as any other planet (4 planetary tiles, build costs, empire wide boni to conquering nation: it needs to be hard and expensive to take or else it would change hands in every war, not to mention almost impossible to recover from once lost).
This would offer the opportunity to some new anomalies: wrecked planets of this type that offer some research + for any technologies this undertaking would require, some fluff ones that show failed attempts at building one of these by progenitor races, "requests" by the materialist fallen empire to "allow" a pop to settle there to study the planet and the population interactions, a broken-open planet of this type that was once functional but has been cracked by an enemy when taking it was too hard/impossible, etc. tt.
It would also be an opportunity for a new one-world Fallen Empire, leviathan or enclace (leviathan: a mobile world of this type housing a hivemind that travels from system to system and eats gas giants for the resources required to keep moving, contact it to trade 10 years of constant resources for possible tech with a chance it might stiff you or kill it by invading it to gain a functioning hive world of a random type rather than having to build one).
TL. DR.: Just shooting the shit about how a massively huge planetary city could function in a vidja game, thank god I am freelancing or my boss would fire me for the time I spent on this.
Edith: Boy, this escalated quickly.
Edithth: I mean, this really got out of hand fast.
Ediththth: Why do I now want this more than the shroud, dammit.
