I think the second point is saying that you can use Master Crafters to offset the downside of war economy - just switch it on in 2200 and your CG production is still good enough, but you get +25% to alloys.
This only works if you assume that other empires don't run war economy though, which isn't a good assumption.
You can do this, but it's a significant loss in pop-efficiency, and doesn't really jive with any build. If you're a war build, you shouldn't be producing enough CG for the difference to matter- the CG margin is less than 1 CG per pop employed, and you shouldn't even have 6 artisans if you're prioritizing alloys. If you're in a tech build, you shouldn't be militarizing the economy in the first place.
Militarized Economy is exceptionally strong in trade builds because TV converts to CG without being affected by the CG penalty. But if you're running a trade build, you don't actually need or particularly want Masterful Crafters, since trade jobs are still more pop-efficient on the low-habitability worlds you prioritize them on, and the point of a trade build is to free up the high-habitability worlds you would be using for upkeep purposes (minerals/CG/Masterful Crafters) for other things (the scientists funded by trade CG).
I like to put my researchers in spare building slots across my empire - the research world designation isn't powerful enough to justify only allowing researchers there.
If you put a researcher in a free building slot on a non-tech world, you spend an additional 0.8 CG in upkeep (assuming no other modifiers), but don't have to spend 500 minerals on a city district for your research world and 2 EC on its upkeep.
The issue with researchers everywhere is downstream of habitability, not upkeep, though habitability does effect the pop (as opposed to job) upkeep.
Habitability is decreasing the pop output efficiency of all non-trade jobs, science/unity and CG/alloy and miner/technicians, and the reason science jobs should be concentrated is because they should be concentrated on the high-habitability zones. However, this brings back the issue of what do you put in your limited high-habitability planets, and where you're getting your minerals from.
If you're getting minerals from 60 or below worlds, you're facing 20+ job output penalties on what's already one of the weakest jobs, and you'd be better off just letting your homeworld be miners. If you're getting minerals from your 80-habitability guaranteed world, you're not getting the bonus building slots on that world and have to build the urban district anways. If you're building the industrial districts on those 60-habitability worlds, you're again facing the same inefficiency not just to the CG-artificer, but the science labs... when you're not using those building slots for amenity workers. And that's not cover the issue of 'building 1500 minerals worth of industrial districts and 36 minerals a month of upkeep for 2 science jobs,' or that as a (usually) upkeep-only resource you want as few planets dedicated to CG as possible, meaning that instead of inefficient scientists you want to use all the pops on the planet to build more CG for the empire as a whole.
It's never about maximizing the science per planet, but the empire as a whole.
Fundamentally, the civics that give free building slots from districts don't change that you want to hyper-specialize planets for pop-efficiency. If you have a CG world, only employ non-CG jobs once the CG capacity is filled. Don't spread industrial districts around the empire needlessly.
Luxury housing and strict hyper-specialisation will net you the most output from your pops, but burns a lot of that advantage in resettlement time and building costs. A pop that waits several months to start working and has a 500 mineral debt to cover is going to take a long time to catch up to a fractionally less efficient pop that got going immediately and for free.
The cost of a science lab, luxury housing, and amenity jobs (holotheater or gene clinic) and another industrial district or CG factory are all base 500 minerals for tier 1. There is no mineral debt.
If your planet is in an amenity deficit, then unless you're specifically going for certain sorts of negative-amenity rush strategies (which wouldn't be doing Masterful Crafters in the first place in favor of better war synergies), you will prioritize the amenity building over the science lab regardless. There is no mineral saving, and only a pop-efficiency-vs-energy tradeoff. Since Artificers produce their own energy, 6 artificers can easily cover their own industrial district upkeep and the luxury housing with energy to spare.
If amenities are not the deficit, and only employment is worth considering, then the substitution isn't between a science lab and luxury housing, but a science lab and another industrial district. Empire-considerations still want as few CG worlds as possible, so that one planet can support all the others dedicated to their own thing. There is still no mineral savings overall, and really a mineral bias towards skipping the science since the most efficient mineral usage will come from both a dedicated CG world and using minerals saved via efficiency for a dedicated science world elsewhere.
Only if the empire as a whole has a CG surplus would it make sense to stop expanding CG production on your CG world in favor for science... but this, itself, should only come after the Capital is de-industrialized. The capital's 10% production output isn't as effective as the 20% job upkeep reduction of 80% worlds, and so rebalancing it from an industrial world to an urban world should take priority.
However, scenarios two and three are functionally pre-empted by scenario 1, and amenities are always going to be fighting against a deficit that doesn't justify scientists being employed unless you already have the extra 1000 minerals for an urban district and entertainer. At which point the argument on mineral savings is worse than dead, but redundant.
At 80 habitability, non-slave/resident pops are going to be needing 1.2 amenities each, such that 3 industrial districts that unlock a building slot require 6 pops who will need 7.2 amenities. Luxury housing will be 5, so net 2.2 amenities required per unlocked building slot even on the best of early-game worlds.
The Tier 2 capital provides 11 (6 from ruler jobs, 5 from capital building), 2.4 of which will be consumed by the politicians, and another 1.2 from a roboticist assuming normal non-rush builds (which wouldn't use masterful crafters instead of other civics). Which leaves 7.4 excess amenities. But another 2.4 are committed for the 2 Artificers from the CG-factory building, which will eventually be needed, especially when that upgrade comes along. This leaves us at 5 excess amenities after we use our CG factory slot.
Well, 5 amenities covers the luxury-housing gapped amentity deficit of 2.2 per 3 industrial districts for 2 more building slot unlocks after the first, ie 9 districts. So, if we use our building slots for luxury housing, we can get away without a amenity pop until about-
9 districts for the 3 unlock (18 pops) + 1 CG factory (2 pops) + 2 ruler pops + 1 roboticist= 23 pops.
At which point we need about 2 more amenities to get us to the 25 pop upgrade point, which... requires investing an urban district for something, unless we eat the amenity cost and rush the last 2 pops over for an upgrade.
By contrast, if we substitute one of those early luxury housings with a science lab, we have a 7.4 amenity swing, as +5 amenities becomes -2.4 amenities. This will require we build an amenity building, which in turn requires either giving up the roboticist- a no-no for econ blooms- OR spending the minerals to build an urban district and another building, and much earlier than the 23rd pop.
But if you're going to spend 1000 minerals to unlock a building slot and employ an entertainers, you could just do that on another world dedicated to scientists.
If you're doing the necessary conquest for 6k research by 2250, that speed is valuable.
It's a slowdown, frankly.
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