So many aspects to discuss about the Hogwarts Express!
I think the HE stations will act like another park exit/entrance, and will probably have park exit signs to make it clear. So, instead of walking to the regular park exit, walking over to the next park, and scanning your ticket and fingerprint to enter the other park -- you'll just do all that here at the station before entering the queue for the train. I don't think you'll have the option to ride without a ticket to the other park, whether in the form a 2-Park Pass or an Annual Pass. That would mean having a ticket booth within the station to upgrade your ticket. I don't get why people say multi-park tickets wouldn't work, when they've been around for a long, long time before something like this even came about.
Now, queues. I doubt this will ever have Express. I think it'll just be stand-by and maybe single riders. Once you get to the loading platform, I think they'll have this very organized, and line people up all ready to go for the next train, just like on rides. So actual time of people loading into the train will be very short. Unlike monorails where it's a mess of people all trying to get in at once. I think it'll have to be very organized to fit the seating arrangement within the train.
I think having three trains would work perfectly, since one train can be at each station, while the third is running in-between. And just keep that rotation. Perfect!
The only thing I am worried about is people with strollers and wheelchairs. Although they will probably have this figured out, with a special place for them in the train cars. Maybe there will be a car in each train that will have an empty row where these could go, or maybe even a space in the back of every train car with seats that can be pushed into the back "wall" of the car to fit wheelchairs and strollers.