While there's something to be said for intuition, as a scientist Sam likes to have hard evidence of such things. That's why he phrased his statement the way he did -- all they really have is faith, as there's no real evidence pointing one way or another. Perhaps if the Pokeball had some kind of indicator showing what's inside....

"Can I take a look at your Pokeballs? Perhaps they're different in my version of the world." As a show of good faith, he fishes out Dragonite's Pokeball, and holds it out in invitation of the inverse; Lance is welcome to look at his, too.