Erm. You're supposed to. That's what pause is for.
Ignoring that pause isn't a viable options playing with other people, the existence of a pause function isn't an excuse for some actions taking inordinate amounts of actual player time. In my limited time to play, I don't want to spend too much time micromanaging pops. Right now this means accepting that I have to accept inefficiencies in order to avoid the UI issue.
In order for the economic changes to be meaningful, it has to punish you for playing poorly. Otherwise it really would be meaningless micro. But choosing when and how to construct buildings is now more of a macro decision on the same level as deciding where to deploy your fleet, since it has real consequences. When mismanaging your economy can lose you the game as surely as mismanaging your fleets, you know they succeeded with their overall vision.
And if you have 50 planets and don't have a large enough surplus/stockpile/money for the market to handle building and upgrading buildings, what are you even doing with all your planets? I get to the point where I can easily absorb the shifts of creating a few specialist jobs around planet 5. Also, learn to know when a planet is "done." Not every planet needs to be built up to 80 pops. After a certain point, you should be willing to stop growth so that a planet can just do what is supposed to do and not need additional information input except occasional resettlement.
What constitutes poor play? I agree that adding and then staffing a ton of specialist jobs so your raw material production tanks is poor play, but making a system that requires a bunch of micro to accomplish "steadily add specialist jobs" isn't exactly leading to good play. A system that requires me to check back every few minutes to execute this seems like it should be in an RTS, where efficient player action is part of the skill. It doesn't belong in a GSG/4x.
Regarding large numbers of planets and supporting a big specialist shift, yes, you absolutely can absorb the impact of swapping workers to specialists if you are floating extra resources and production. If you aren't, or are adding quite a bit more specialists, you can still run into problems late game. And no, this isn't a planning problem because it CAN be mitigated with a boatload of clicking.
I don't think you're supposed to have that sort of control, your pops are supposed to represent blocks of autonomous people, you can't necessarily order them where to work.
I would support adding this level of control to hive minds, though.
You can achieve this level of control over pops within the existing UI, it is just very time and action intensive. The UI should be improved to make it easier.
Also, gestalts can already freely move between strata without any negatives. Thank god, since their baseline colony capital buildings have so many non-productive jobs.
I honestly don't understand why you would build a building if you don't want pops to take the jobs.
Do you want the game to magically know when you want those jobs taken? Otherwise, even if you have the building pre-built (and you can disable buildings or their jobs, fyi) you still have to go and tell the game you now want those jobs taken. which is basically the same amount of interaction as just going and building the building.
I do agree the priority system is bad, though. It should let you order the priority of the jobs, with the most important showing at the top of the UI and the game should then fill those jobs in order of priority.
Short answer - I don't want to be spending a lot of time interacting with this planet after I've decided how I want it set up.
Long answer - If pops did not autopromote, as in only new pops would take higher strata jobs, I could queue up buildings instead of having to come back every 10 minutes or so. The checking up isn't so bad early game, but once you start owning significant parts of the galaxy it feels like a time suck. With current UI, your options at that point are to either suck it up and take the econ hit while your new pops fill out worker jobs or wait until you have excess population then add the jobs.
With an autopromote toggle, turning it off would mean I could queue up those specialist buildings and expect those new jobs to be filled every 20 months or so. With the addition of a better job priority system as well, I could implement my economic plans easily and with minimal player work, freeing up time for 'diplomacy' and other pursuits.
I think an example would be helpful. In one of my games I have a mining world that is almost filled up. I'll have lots of extra building slots left once the resource districts fill up. Adding T1 alloy foundries makes sense here - they're relatively low upkeep and I could use more alloys. I could reasonably build 3 to add 6 metallurgists. It is ~1100 minerals for the foundries, so being able to prepay is pretty trivial, as is the energy upkeep. Miners here are making 8.5 minerals each and metallurgists consume 6 minerals each. If I queue up the three foundries and swap 6 miners for metallurgists, that's a fairly rapid 87 mineral/month swing. I can absorb it as my current income is +250/month, but I have more than one world that I want to start adding finished goods production to, especially as additional resourcing colonies are developing. Autopromote off means that I have a steady ramp up of -36 minerals/month over the next 10 years instead, which means I can easily queue up specialists on most of my early resourcing colonies.
I could just micro it and build an alloy foundry every 3.5 years across 4-5 colonies, or make a clerk building as a worker holding pen and revisiting the colonies in 10 years to swap to alloys, or just give up on the whole endeavor and take actions to boost emigration to central production worlds. But why should I have to do that when a damn toggle saves all that work.