I posted analysis in the science thread that 50-80% of science comes from undeveloped sources in the unmodded game
No you didn't. You posted an analysis that said 50-80% of science comes from undeveloped sources in the unmodded game *in the very early game*. Not true once you have scientist specialists, academies, universities, public schools, research labs, etc.
And then you shifted away from that model already by adding the mentor's hall.
Consider a size 15 city with mentor's hall, library, and university.
It has 40 science. Only 37.5% is coming from basic population.
Add in a 5 research academy and 2 scientists at 3 science each. Now only 15/51 = 29% of science is coming from basic population.
Most of the game does not occur pre-medieval era.
Science on villages is not needed to have only a moderate amount of science coming from basic population.
I also don't see that reducing the yield from basic population is necessarily important, because population is not "basic", it requires investment (in farms, happiness, food generation buildings).
If we never build villages (like in the unmodded game), our options are limited to farms and mines
Who never builds villages in the unmodded game? In almost every wide game I play I'll concentrate most production in large specialist cities, while other cities are mostly for happiness/culture/gold and stay a moderate size.
Who would never build villages if they have 2 gold each, rising to 3 gold? I build villages in (the older versions of) VEM all the time.
In Communitas our choice on hills is usually between a mine or village, and on flatland we choose between a farm or village. This leads to about 2 choices per tile, with similar importance, and different bonuses.
How is this not true in a world where villages give gold and only gold? There are still 2 choices, with similar importance, different bonuses.
In my version (and the core game version) on flatland I can choose to go for more science (buildnig a farm) or more gold (building a village). There's a tradeoff. In your version, both choices mean more science.
You keep posting your bell curve, but the figure is wrong when you mislabel the axes. In my version, in the middle there is a tradeoff; you can get gold or food. But your version is on the dull right end, where both choices lead to science and gold (farms lead to gold via trade route income).