They can advertise that the Hogwarts Express train will take you to the entrance of the Harry Potter section of the other park. Once you arrive, you'll naturally need a ticket to be admitted to that other park.
This is exactly my thinking...the theme park geeks like us will know that this is no ordinary train..the casual public will just see it as a means of transportation if you have a two park ticket.
I am positive that every cashier will be trying to upsell the experience to buy the two park pass.
Saying it causes the same confusion is incorrect. People will definitely be confused on why they will have to "re-ride" the train, instead of just staying on board and going round trip.
Keeping the HE as a two park pass is the smartest way to handle this new ride/transporation system.
I'll probably take some heat for this one but...
the absolute easiest solution would be to only sell 2 park tickets. Just pick a date and only sell two park passes from then on. You would of course honor any 1 park ticket holders to both parks until they eventually fade away. 2 park tickets aren't much more expensive than 1 park passes at this point anyway. Not many tourists travel all the way to Orlando and only do ONE universal park. A lot of locals have APs anyway...
For a family of four it will cost them an additional $80 to do the same vacation if they do this. So a family of four plans to do one day at each park, so they get the two day single park tickets. Spend one day at IOA and one day at Studios. Pretty reasonable and what I would do. Why do I need to hop back and forth each day? That might be a hard pill for some families to swallow.