PaperBeetle
Emperor
If you MM citizens after growth, I don't think 'emphasize food' is ever worth choosing. The new citizen will get born, assigned to a high-food tile, and then get moved before he has a chance to work it.
If I were to change the 'emphasize' option, I'd put 'emphasize commerce' in my specialist farms - that way, I might net the occasional extra gold piece.
Commerce is calculated first on an empire-wide level. Then the game goes through each town, first adding food then adding shields. So if you are prepared to micro your towns immediately after growth, the only resource that it is worth emphasising is shields; by the time the new citizens gets assigned, both commerce and food have already been dealt with.
Note that this interturn order gives plenty of opportunity for Gold Mine-type exploits. Consider: despotism, C3C, 2 turns left to go on a tech. You could probably get a lot more beakers by switching large numbers of citizens to scientists. You could switch enough to get the tech in 1 turn, and still use the Big Picture to get into the city screen, and set all your scientists back to working the land before food and shields are counted.
I wonder, is it also true that although beakers and coins are counted up first, happiness isn't counted until the city-check phase, so you wouldn't have to worry about keeping your empire happy the turn before getting a new tech? Just do it in the Big Picture instead?