It's very difficult to get most of your cities at their ideal size for running specialists "in time" let's say for a golden age switch, hence farms. Having to run hereditary rule hurts cottages, but it also hurts high food cities if you don't aggressively split up the food. But then the new cities need granaries and time to grow, and you're back to the farm problem. Farms often have more happiness cap problems than cottages. Cities with "too much food", it's often better to scale back from farms to cottages, or all the way to mines. You can run the slider, but evidently even hammer economy enthusiasts do appreciate their trade routes, and they may not want to crank it up too high. Multiple great person farms are only inefficient if they don't produce a great person, or if the multipliers (actually the great person costs) are so poor that you'd get more out of using the population on other things. A marginal city that eventually produces a great person is efficient, so long as you switch them off after you pop it.