If rune scarcity is your main concern then lets just change the rune formula instead so that there isn't a cost malus below ~1k acres, just make it a set X runes/acre or per nw formula. (at the moment the formula is a curve which benefits larger sizes more than smaller ones)
This is one of the major points against starting size, because the farmouts are going to be even bigger, and getting an early farmwar is going to be a bigger factor.
No, absolutely not, if this power should exist then it should lie with the province owner, not the monarch. Nobody other than you should be able to decide how you run your province. Of course team play means that most turns some of these decisions over to a monarch or strategist etc, but this should be your choice, not theirs.