I think it depends on more factors.
1. If the city is in an alien world (not our known earth) then it is reasonable to allow the player to build things where they see fit. However if you are using a world with a known civilization (Greeks for example) then you should limit the building types per plot to what would have logically made sense for that culture/civilization. If the civilization/culture of your game has been fleshed out by you, then the same rule would apply. It simply makes more sense that way.
2. Rebuilding and new town does need to be considered. Often, but not always, the same building is built over the ruins of the old. If you are rebuilding, but allowing different types to be placed on the plot you have to ask yourself, "Why?"
3. How extensive is this town? Is coding an 'anywhere' town going to be more trouble for you then it would be worth? (I've an idea that is what you are trying to determine.) Is it actually a hamlet? A village? And so forth. (In Europe, the difference between a hamlet and a village is the presence of a chapel/church. Difference between a village and a town is the presence of a market.)
My preference depends on how it is presented to me. In 'Harvest Moon, A New Beginning' I was a bit annoyed at the 'place buildings anywhere' method because of how cumbersome the edit mode was. But that doesn't mean I am personally against the concept of it.