I wondered about that myself. I don't see why it would make a difference, other than:
When you look at the film and you can read the numbers, the emulsion side faces away from you. If you put the film into the PrintFile this way, the script and the numbers are both readable. PrintFile claims that you don't need to take the film out to make contact proofs. They make more sense when all is readable and nothing is reversed.
Just guessing ,but it works for me that way.