As a programmer, you have to be able to see all the possibilities and code your product to be resistant to wrongful inputs. These games are definitely not.
Visiting active places in an order which is different from the order they were added is hardly considerable a "wrongful input".
It's a bug.
Either you foresee all the possible paths and code different dialogues consequently (which is a hell both in programming and in storytelling), OR you only unlock the places in the correct order.
And in the latest case the "sandbox" is just an illusion. It all boils down to a multiple choiche based VN with a series of forced clicks to move around on the map in the only possible order.