Ideally, three-button suits aren't supposed to have the top button fastened, either; leaving it undone balances the look and permits the lapel to roll closer to the waist, where it should be. In fact, the two-button suit takes care of this nicely by removing the offending button altogether. It is possible, if inadvisable, to button the top button without violating fashion rules.
There are a few exceptions. The bottom button on some double-breasted jacket is buttoned. There is also a type of custom jacket called a "paddock coat," where the placement of the buttons is altered and both are buttoned. John F. Kennedy was known to wear such a jacket.