Logistics is one thing, but they don't want to force people into 2 park passes for one ride. Lets play out this scenario.
A family of four is looking to spend two days at Uni, one day at Sea World, and 3 days at Disney. They go to the gate the first day and buy that one day one park pass, because tomorrow they can visit the other park. They go around and do a bunch of stuff and get to HP, they realize they need a 2 park pass to ride HE, they upgrade their pass. They do a bunch of stuff in IOA and realize they don't really need to come back a second day. Instead the day before when they went to Sea World they got a 2nd day free, why spend more money to come back and do stuff again or stuff they were not interested in, when they can go for free to Sea World. So now Uni looses out on the 2nd day pass, the food, beverages, etc.
Do you see why financially it does not make sense for Uni to only allow 2 park passes to be the ones to ride HE. They would rather people spend two days (one at each park) then spend one day at two parks. Uni is trying to make a resort where people feel like they need to spend more than one day there. Not think they can only spend one day there. More people than you think have one day one park tickets.