Why is it more a problem to turn into game term than a completely disconnected from reality science-alone tech tree?
CIV6 is already like this, and I dont see the average CIV player horrified by it.
You keep acting like having just science in the tree solve some problem, but it does not.
It works for devs and most players, in a game that want separated elements for separated victories.
We certainly do not need separate biologists and botanists.
Why "certainly not"? Separated musicians from writers worth it when can be easily abstracted as Artists. Geological or Biological expeditions worth the same than Archeological expeditions, even most if Science victory is about colonize a different planet.
Temples and monasteries should produce culture and monasteries could produce science although that may be best associated to a civic or religious belief.
Every culture in the world have incorporated their early explanations of social and natural phenomena in their beliefs, ancient temples show a close relation of mathematics, time recording and astronomy to religions. Temples should be one of the earliest buildings on game and produce science by default even if is a little.
The rest of your questions are completely irrelevant to the notion of a science-only tech tree - they're whataboutism,
The idea of separate Tech and Civic trees is related to different ways to achive victory. If you want to change that it would affect the others aspect that could need some adjustment.
"these other things are flawed so why are you criticizing this flaw".
I am suggesting to change all those flaws in terms of unique gameplay. Turn ideologies into significative responses to your social changes, narratives from the interactions of your own pops and diplomacy.
More unique mechanics do not mean isolation, for example Universities and Temples could still produce Great Philosophers that provide free Ideologies to implement. A empire of multiple Heritages (cultures) would trigger events about Pluralism vs Unitarianism, or the lack of Amenities/Services would cause discontent in the Laborers of your many Factories, then a Proletarian Movement. New Techs would still be an element to unlock some Ideological Revolution but they would not be anymore pure accumulation of science or art(as is represented in game) to click a button in a boring tech tree.
You can build a ICBM being communist, capitalist, fascist, a monarchy, republic or even a theocracy, but you can not build the same ICBM without develop rocket, computer, radio, etc. Still a world with ICBM from rival nations would trigger a Disarmament/Pacifism ideology event with some nice diplomatic bonus.
So excuse me but I find more interesting as gameplay design, also more respectful of the history dehind civics/beliefs to have something beyond more "techs" to expend points in a boring tree.
Do you know what? There is also this. You can use a Great Person (Scholar, Philisophers, whatever) to found Academies
in your Universities (for a max of 3 or 4 each one). These academies would be named by their kind for example Economy, Theology, Biology, Astronomy, Chemistry, History, etc. And of course each kind have different bonus.
So here you have, a way to point the role of Social Sciences in universities without go back to a deterministic and boring civic tree (also save us from whole disciplines as "techs").