Actually, having reflected on this for a bit, this is exactly the fallacious thinking that leads to conspiracy theories and religion.
I think the wonder of a 6-year-old who hasn't yet learned that there's usually a mundane explanation for magical things is a good thing to be around, but we have to be careful not to make the mistake of going from "what an interesting way to look at the world" to "what can we ignore to make this an actual possibility".
Bad Science takes a goal, then ignores (or discounts) any evidence which contradicts that goal; Good Science (as has been neatly explained on this thread) takes the goal - the "hypothesis" - and sets out to DISprove it. Only when the best scientific efforts to reject something have failed can it be considered to be anywhere nearer "proven".
So yes, all of the atoms in the universe could be expanding against some outside frame of reference. But we cannot speculate on what that would mean unless we can measurably and demonstrably demonstrate it - until then, that idea, and any deriving from it, are only notions with no scientific validity beyond their curiosity.
Similarly, it is possible, by excluding various factors and observations, to conclude that the Earth is flat, or even shell-like. But if only one factor or observation contradicts that, the shellworld theory has to be re-examined to take that into account. Or, of course, the observation can be demonstrated to be false, but what it can't be is simply discounted.
That's why scientific integrity is so difficult to achieve, and so tempting to swerve - it only ever takes one thing and the whole show comes to a grinding halt.
And, even if there's nothing to disprove the theory (I'm looking at you, string theorists), you're still stuck with the necessity of providing experimental observations to back it up. We're unlikely to be able to build particle accelerators of a size necessary to produce string objects on demand any time soon, so we're forced to rely on natural phenomena...but we don't quite know what a string-producing natural phenomenon would look like (though there are quite a few theories), so it's hard to know what to look for. It doesn't mean string theory is wrong - and it's a very appealing and tempting notion that it could be right - but until we can come up with something to show, repeatably, that the predictions for the theory hold true in fact, it's only a theory.
Same goes for shellworld. Except there's rather more to show that the idea is not factually correct.
But good luck explaining that lot to a 6 year old. Let him hang onto his magic for a bit longer.
