IMHO, you are over-complicating things. Just build the two tracks on the Jefferson extension. With the smaller trains, you are going to need more frequent trains - there are only so many bypass points you can build. The Jacksonville Skyway shows you can build one row of columns for 2 tracks see below:
Also, the same system shows how you can make one transit station - without double elevators and stairs - for two tracks:
Yes, you would need to build a turnaround loop for the trains to go back the other direction. I don't think that's a big problem, the trains are so small a turnaround wouldn't be that big.
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