The story UP gave to BART was that they were planning to resume freight service on the Mococo. I didn't believe it then, and I still don't believe it. There are no passing sidings between Antioch and Tracy, there's no ABS or CTC signaling system, and the tracks use bolted rails and wooden ties (low speeds). Sidings and CTC would need to be installed in order to run trains in both directions.

The bridge over Mash Creek in Brentwood would also need to be repaired or replaced. It was damaged by a grass fire several years ago.

I think BART wants to keep e-BART grade-separated from vehicle traffic, although it's not really necessary. By keeping the e-BART trains in the freeway median, you maintain that grade separation.

BART would have a difficult time proving an eminent domain case against UP, especially when there are plenty of other options for right-of-way.