From my understanding of the project, all of your concerns are, well, not concerns.

First, we have existing termini that are pretty dang close to the respective city centers. LAUS is within walking distance of downtown L.A. (and is connected to the Red Line subway, anyway), and SF's Fourth and King Caltrain station, which is where I'd assume the HSR project would terminate, is within walking distance of SF's major business areas and is attached to a Muni line.

The "bullet train" would make limited intermediate stops, as well. A CA-99 alignment is more likely than an I-5 alignment, which would take the train through Merced, Fresno, and Bakersfield.

Last, from what I understand, the line would use a dedicated right-of-way not shared with freight service (with the possible exception of connecting tracks within a mile or two of each respective terminal). Slower "local" passenger trains and commuter trains might use the tracks, but no freights. The only thing the UP has to do with CA HSR is allowing the HSR project to use its land and parallel its ROW. That seems to be the problem they're complaining about here: allowing the HSR project to build its ROW on a second (or second and third) track next to its slower single-track mainline and that the "200mph" (not sure if it'll be that fast) will cause freight cars to get knocked over or cause lots of damage if trains are derailed and jump the tracks.