If the system was somehow built like that, the whole thing would need to be operated as one system. If one station needed to be stopped for whatever reason, the whole system would need to be stopped.
This is exactly the problem. A line has a specific number of cars at specific spacing. Trying to manage between two lines messes with this. There's no easy way to solve the issue that doesn't also tie all operations of both lines (speed, stopping, loading) into a single system.
And, we've already heard that even switching out 2 cars, 1 for 1, on a single line isn't something that's normally done without stopping the line.
The way its going to be, you will only transfer at most one time no matter where you are coming from or going. The only thing that concerns be is the DRR station, and how it will impact people trying to board there if cabins are already full, assuming they don't make everyone get off there.
Radios, phone lines, buttons on control panels, cell phones, something like that solves the issue. If DDR has a line, the cast member at DDR communicates with a cast member at the earlier station and they let an empty car go through. If it's a big line, they let a bunch go through, probably every other one for a bunch. It does mean that getting on at DDR could have a short wait, however long it takes an empty car to get there from the prior station. When the system isn't totally full, there will be empty cars, or guests getting off at DDR creating empty cars. At crush time, they just need to create that same empty space artificially.
I expect every car to detach, move slowly through DDR, doors open and close, reattach to the line, every time they transit through DDR independent of if you get off or stay on. In fact, at the Boardwalk turning station, I expect every car to detach, move slowly through the turn, reattach. Without the doors opening, but with the ability to override and open the doors in an emergency evacuation if needed, with cast member support. In fact, the cast member at the turning station will probably be the most bored member of the team with nothing to do when things are working normally.