Isn't the point of what an illusion is though?
When a magician makes your card disappear then reappear, you know it's not 'gone into thin air'. You know you've been tricked. What you don't know if where your card went, and how it got there and back. That makes you think 'maybe it did go into thin air'. It questions your rational judgement.
It should be the same principle with Ghost Train. You know you've moved, that's why you're in a different place (and later return to the same place). But you don't know how you've moved, given you're in a train suspended in mid air. So it makes you think you did stay in the same place the whole time, again questioning your rational judgement.
The trouble is, as you say, that whole point is completely lost. You don't have enough time to appreciate that you're boarding a train that's suspended in midair. And when you leave, you leave too quickly. There's no reveal about it. You can't question your judgement if you don't have enough time to make a judgement.