Mining autoprogress is a way to automatically dig down when you are on the deepest rock. The limit is the maximum amount of seconds the next rock can take to break for this to work. So if you put in 90 seconds it would keep digging down until it would take more than 90 seconds to break the next rock.
Ore clumping may be inefficient now, but that will change later in the game!
In the village, resource caps are a lot more important than in other features, which is why about every second building increases it. Buildings like farms, plantations and mines have the benefit of being persistent, which means that they stay even after prestige. So yeah, the village is intentionally slower than other features.
School is something I'm already working on, I simply did not expect players to grind that much for the time skips, so there will be some sort of limit on the amount of times you can play for these rewards.
Gems are (like the village) supposed to be one of the slower features, as they are meant to be a resource you really think about how to spend