Yes, the player can capture broken colonies and they'll keep working... you just can't make them yourself via normal gameplay.
IIRC even the vanilla game has one or two of them, the most obvious being the Hegemony capitol world which has every facility in the game stacked there, limits or logic be damned.
The problem with the idea of the "one colony to rule them all" is that they invariably, nay, by design must turn into a 100% export based economy. They will import literally nothing if they can produce literally everything, and this is bad for the game's overall economy as a whole. This is probably why the dev put those industry caps on worlds to begin with.
I mention this because, as I discovered the hard way through various wars, when I started nuking my enemies out of existence the income of my colonies fell away to nothing because there was no one left to buy my stuff. All that surplus was just rotting away in warehouses and colonies that had an income over 100K dropped to under 20K in less than a year.
So what is most likely to happen when Das Ubercolony becomes the "last man standing" and defeats all their enemies? They sink into bankruptcy, because the upkeep on twelve building slots crammed to the max will likely be higher than their tax revenue, and without anyone to sell to tax revenue is all they get. Maybe a planet with a habitability rating of 50% might be able to survive, but 200%? Forget it - they'll sink under the weight of their own excess very quickly.