If the train goes between parks, it is a form of transportation, not simply a ride. And I didn't say you'd be able to ride endlessly in my theoretical. The people with tickets to a single park would get off when they return to that park. Not that complicated.
Expanding Potter into USF is certainly a strategy to increase that park's attendance and encourage park hopping, but they still have to cater to people with single park tickets. Not doing so would result in a loss of $$$.
Actually, I'm not sure that doing a half-and-half train would work from a logistical standpoint.
Let's say you load the train in USF. The front half are people who have park-hoppers and will be allowed to get off the train at IOA. The back half are single-park people who are riding for a round-trip.
When the train gets to IOA, the front half empties and the back half remains. But now you have people coming from IOA to load onto the train. Those people will also be made up of some riding round-trip and some riding one-way. You'd have to put the round-trip people in the now-empty front half, and try and fit the one-ways in with the USF round-trippers in the back. And once you open the doors for the USF round-trippers, you all of a sudden introduce people hopping off and trying to get out into the park.
Groupers on the platform wouldn't be able to efficiently group people for each car to maximize capacity like the express and Epcot platform monorail CMs at WDW. It would have to be an open free-for-all like the Resort monorail platforms.
The best logistical situation would be to empty the train out every time it pulls into a station, and make anyone who wants to ride round-trip get out and get in line again for the return.
And if they require a park-hopper ticket, they'd better include a way of adding park-hopping to your ticket there at the stations, either a staffed Guest Services window, or a ticket kiosk. Otherwise you'll have some pretty ticked off Guests when they're told they have to hike back to the front entrance to upgrade their tickets...
-Rob