Now, I totally understand what you mean. To what extent do you think the type of preposition to be used depends on the main verb in the sentence?There are certainly conventions of usage that depend upon the object of the preposition. In a car, on a bus, etc. But you can't say that this is a universal rule.
Much of the use depends upon the intended meaning as well. In the box, on the box, at the box, near the box, by the box, etc. are all possible.