That's what I and I imagine most of the players were and are hoping for. Really, the game probably needs both: some system that represents the overhead of such a large empire by making some things like unity generation less efficient, and some mechanic to represent instability due to internal conflict.
For the former problem (sprawl), I guess it's easy enough to represent that by tech and unity cost penalties. A more realistic system would probably just have different tech levels per planet and some "cost" to propagating it, but I can't see Stellaris ever implementing something like that for sanity reasons. Unity is such a vague concept that I don't know how it would be implemented differently unless it too was per-planet and factored into planetary stability or something, with the unhappy pops costing unity upkeep like an earlier dev diary proposed.
For the latter problem, people have been screaming for internal politics since the game was released so it's starting to look doubtful that we'll get anything substantial considering the other DLC that's been developed before it. I have some hope that the "situations" concept that they've proposed in recent dev diaries will give at least some flavor to that, but my guess is that it's not going to be that sophisticated. It'll probably be something like galactic stock market crashes that cause a big penalty to your trade value or something. Supposedly it's based on a system from some other game of theirs that I haven't played so it's probably not going to be a real mystery what it will be for anyone who is familiar.
Internal politics will be hard to implement in an interesting and not frustrating way I guess, similar to espionage, meaning it probably won't ever have real teeth.
The problem with Paradox is they are too multiplayer focused. You can tell because of their extensive use of "Mana". This is basically a boardgame design concept, obviously it isn't actually called "Mana". And boardgames are almost always multiplayer, except some of the nicher economics only games.
Unity is mana. It is a "balance" shortcut as well as a multiplayer thing. In a boardgame the player meta play replaces internal or even external interaction. Same for Dev Clash. No one cares about what the AIs do in big 20+ player Dev Clashes. But even most people who have a normal amount of friends don't have 20 Paradox Bros to play with.
Prestige and Piety are distinct from "Mana" to be clear. You gain them by doing prestigious or pious things and they provide relevant bonuses and in cases where you can "spend" them you do it for flavor relevant reasons. Although I prefer penalties associated with actions that have other costs rather than direct costs for these non-mana resources.
To have good internal politics you need a system just as deep as the combat systems. Which is pretty deep or at least complex given that Paradox games are map-painter war games at their core. The same applies for diplomacy and for espionage.
Another issue is the market. The market for shallow non-combat mechanics on top of core war-games is large. The, current since a really good example could grow it, market for attempts at deep non-combat mechanics is vague and amorphous. Maybe it will coalesce if you make a good politics or diplomacy game or maybe it won't.
Maybe you take that risk if your top guys aren't multiplayer focused but as it happens they are so Paradox won't.