While we were watching, I told Michelle & Kira to listen for how and when people mention the Conductor when he wasn't around. It turns out that this was pretty easy, as it's only twice. Both times the Know-It-All refers to the Conductor as "he" when talking to the Hero Boy. Those are the only two in the conversation when it happens, and no one else is listening in. The reason that we see and hear the Conductor as we do, is because we're privy to the Hero Boy's experiences and not someone else.
Now for my theory. It's my belief that the conductor appears to each child as themselves as an adult. That's why they tend to trust him and what he says. That would also explain why some kids, like the Know-It-All, are happy to receive praise from "him", when they normally wouldn't care. Of course, this raises more questions, like is this one of Scrooge's ghosts or something else? Regardless, I think that this adds a level to this movie that I'm not sure the producers intended when they made it.