Yes. "Alatt" in this sentence would mean under something or someone. Relation instead of location.

In a tiny way, yes. And of course it can also change with intonation. I would say that the difference is negligible but I will try to give a sense of what it might be...
You know what, I am trying to come up with examples for either one. Like when I kind of expect the boy to be below, I would rather use one version. But then I realize that it is just as good with the other one. So, no, there is no significant difference. The word order just gives a little more emphasis to what comes first.

However, if you want to go wild with the word order...

A fiú van lent? - It is the boy who is downstairs? There is somebody downstairs. Is that person the boy?
Lent a fiú van? - The person downstairs - is it the boy? Kind of the same as the above.

There are two more permutations left:
Van lent a fiú?
Van a fiú lent?
These are somewhat unnatural. But one could argue that, in the right context, these, too, mean something. Like a general question about the habits of the boy. Does he ever spend time downstairs...

Always when talking about the location of an object.

yes

I think here the most important information asked in the question is about the boy's position, therefore the word "lent" (below) goes first. E.g., if you want to ask "Is the boy below?" it will be something like A fiú lent van?