We don't know how they are configuring this transportation yet, we only know the routes. We don't know that it's going to be an off load at the trindad and board anew scenario. It certainly could be.
Might also be more practical to walk from the northern part of pop/AoA to the station at trinidad, assuming there will be a walking connection out of this.
It is rumored that there are 3 distinct lines. It would make sense for one line to be dhs to trinidad station. One line from trinidad to pop. and one line from trinidad to north CBR then boardwalk lot and Epcot.
If that's the case, the bottle neck will be the morning at park opening time. If it's predictable you can plan for it. In that case I think they could channel the line transfer to make it more seamless.
I'm still of the opinion that whatever type of device is used, the line from trinidad to DHS will be a higher capacity than the other two lines. Even if its just a operational speed change. That will effectively reduce the bottle neck.