The key is to... stop caring?

[Xavori]

the filtering seems to stop working once domes start getting overpopulated. Wrong spec won't leave unless there's free space elsewhere for them to move into, prefered professions wont move in if the wrong spec guys are hogging the housing.

Uh. You're not filtering correctly.

1. You must have an old folks home dome. You have to get non-working people out of domes, and you need to get empty specialist slots open so your universities can 'know' which specialities need more colonists.

2. You should be thumbs down on everything in a dome except that dome's speciality.

3. You should have a thumbs up dome for every speciality except medic and security. Thumbs down and thumbs up absolutely will move colonists around.

4. You need a lot of shuttles. This one is totally on the devs for not making a transport layer for their city builder. That means instead of coming up with a nice efficient traffic flow, you just have to brute force it.

 

[Bronzewing]

I've been doing all that, the point is if all the domes are full to capacity, THIS STOPS WORKING. The old folks dome gets full no more will go there no matter if you forbid them from other domes or not. an engineer and a scientists won't switch places if both domes are full and they're in the wrong one because each looks at the dome they're meant to be and go "No space, so I'm staying here". The only time this updates is when a senior dies (one person will move) or when you build a new dome and new housing becomes available. Once again though late game your population can easily be growing so fast that as soon as you build any new housing all slots are instantly reserved for overflow from existing domes.
I had a school dome for example, all but cildren forbidden. Had over 90 youths in it because they had no vacant adult dome to move to so they just stayed there homeless. And because the school dome had mass homeless, no new children would go there, despite being forbidden from every other dome in the colony.
That colony had 60 shuttles running.

 

[Wandering Sentinel]

Well, the solution for the old folks dome if you don't care is to close the valve, flip the switch, and lock the doors... Not a humane one, but it's a solution nevertheless. Besides, as you said late game population can grow fast enough to block off entire domes.

 

[zenstrive]

With everything else being sometimes hard to juggle, sometimes too micromanaging with the human elements is just too tedious.
On my latest playthrough as Europe, being graduated from IMM with all wonders built, with around 200 of colonists I found myself cornered with water usage. My 10 000 water deposit all dried up, and the next one is high north.
I don't have moisture vaporator tech yet.(the fact that it's high in the biotech line is ridiculous)
I have magical drone hub breakthrough.
I have tons of food and fuel though and around 1500 conserved water. So I shut down the farms, the polymer plants, and then the fuel refineries, then string together tunnels and pipes and pipes with RC rovers and cables with rockets repeatedly landing with materials to reach that 100 000 deposit of water.
If by this time I actually care about the breeding-happy colonists, I would kill myself.
I then repeated the same micro managing of resources later when I tried to build mohole wonder because metal deposits are drying up fast.

So on this game, you can actually care about the colonists and constantly pull your hair off optimizing them, or just consider them the biological parts of the Mars conquering machine. They're needed to make things, but that's it. Many of them will not be efficient parts, true. Heck you can ditch them from extractors if you have extractor AI's breakthrough or Mohole wonder.

And yes, this is Tropico in space. But it's even lacking in the presentation of deposits. in Tropico the deposits can be seen with structural presentations (caves for metals, oil gust for oil). Now it's just an icon on the terrain.