Ah yes, Perez, the wikileaks of theme park lore :lookaroun
I took it to be kind of like how the Monorail works at California Adventures and Disneyland. You can ride the monorail back and forth all you want but to actually get off and get into California Adventures you need to have the park hopper. (sorry if it isn't the monorail and is the train it has almost been 10 years since I went to DL).
If they did do the train they would probably have a sort of gate entrance you would have to go through once you get off. I don't know how exactly this would work at Universal but seeing as they are putting so much money into Potter and hoping it brings even more people to their hotels and parks then I'm sure they will find a way.
The monorail at Disneyland provides transportation between Tomorrowland and Downtown Disney. So, you cannot "ride it all you want" without having valid admission. You would obviously need a ticket to begin with in order to board from Tomorrowland, and guests boarding from Downtown Disney swipe their tickets at the monorail station entrance, and then board the train.
From the Disneyland website:
The Downtown Disney District Monorail Station offers convenient transportation directly into the Tomorrowland area of Disneyland Park. The Disneyland Monorail is accessible by Guests with valid admission to Disneyland Park. You must use your Disneyland Park admission before you can board the monorail.
My guess is that Universal will operate their "train" in exactly the same manner - swipe your hopper, and then board the train.
I think that this (HP train) will actually be wonderful for passholders or other frequent park hopping guests, if the wait time isn't too long, because it will actually make transportation between the parks more convenient (much like the added convenience at Disneyland). Of course, lines will probably be long simply because it's HP themed, which will semi-defeat the purpose. If they turn it into too much of a "ride," then they will need to ensure that all guests exit the train on each run.
Actually, I wouldn't be surprised if team members (employees) were to use it on slower days, because it could actually provide for a more convenient method of transportation between point A and point B. Amity is much, much closer to costuming than WWoHP or any other area of IOA.