@Lanefan I appreciate you taking the time to explain your reasoning, and that all makes a lot of sense. I eschew settings with established power ecosystems- I prefer uncharted lands or frontiers because it circumvents all this - so although I'm unlikely to implement your ideals I can at least understand them. When I do run civilised games, the players are usually plucky rebels/criminal ruffians fighting against the system so the 'bigger fish' are the problem rather than the cure.
You don't really NEED an 'uncharted land' for this. You can simply assume that there really are few, if any, of these 'big fish' around. So, lets take Doskvol as an example (and this isn't about what sort of rules you use, you could use Doskvol as a D&D setting without any problem). There are organizations, the books list a couple dozen of them, within the city. They range from 'tier 1' (small, like under 10 people, very limited resources, essentially no power) up to Tier VII (world dominating power, the Immortal Emperor, armies of thousands, etc.). Typical NPC groups that operate in the city and 'do business' there generally range from Tier II to Tier V. I think the local imperial army barracks is basically a Tier V organization, up to 1000 troops, heavy weapons, large funds, highly connected, etc. The local cops are more like Tier III IIRC, each precinct can mass enough men and gear to crush a small Tier I/II gang if things get really out of hand, but you can also escape from them, and if you reach Tier III yourselves even fight them successfully (though presumably then you make enemies of much nastier groups that have law-and-order as an interest, like the Governor and City Council). Most of the criminal gangs don't rise above Tier III (so maybe 100 minions at most), though I think there are 2-3 of them that are Tier IV.
In this sort of milieu the PCs can easily operate, and often with impunity. There's a concept called 'war', so you have a relationship value with each of the NPC groups, and when you piss them off, it goes down, until at -3 they come for you (or at least want to, they might be too weak). War has various negative mechanical impacts, so you generally want to avoid it if you can, though it could be a good move now and then. I mean, some of this wouldn't apply in D&D necessarily, but the idea of this network of interrelated groups of different grades of power, and each with its own specialized 'thing' that it does well, and with its network of allies and enemies, etc. works fine.
Yes, Doskvol does have a few 'high level NPCs' effectively, like the Governor, the Imperial Barracks Commander, the Emperor, and a lot of 'mid-level' guys (city council, Spirit Wardens commander, Church of Ecstasy leaders, major nobles) none of these generally is totally free to act against you, nor do most of them really care what you do as long as it doesn't threaten overall order too much. It would be EASY to get your party crushed, just piss off everyone, but you could also very easily navigate this kind of political system and exist as "just another power center." Probably if the PCs get TOO powerful they'll have to either assert some overt authority, or face being driven out by whomever they are trying to displace, but that should be INTERESTING, as their enemies will be typically only a bit more powerful then themselves.
I think in BitD play the most likely scenario is eventually your crew gets wiped out, or reduced back to 'Tier 0' and that's kind of that, but its not inevitable. A group could rise to, say Tier V, and then just remain as one of several major city power groups.