<<< Some uninformed person at BART was told that passenger trains and freight trains can not share the same track, so thus the need to build a separate set of tracks along the Mococo>>>.

Oversimplified

Unless the LRT- Sprinter -DMU equipment is designed for the same impact loading the two types of vehicles may not operate on the same line. Thus freight traffic COULD be restricted to the non-operational hours of the DMU-SPrinter-LRT, I believe San Diego and Escondido operate this way .
So just say UP doesn't want to be restricted to a few hours a night, on the track they own and pay taxes on. Right now that's a business decision the UP deems better - let it lie fallow and pay the price, rather than the price of getting a few dollars and a giant PITA