I agree that for now Siemens cars look like the best bet for new purchases. Purchases from Siemens might need to be a bit larger than planned, though, due to the need for more cars to make up the axle counts.

Metrolink operates at least in part on its own tracks, but many lines are on UP, BNSF, or both at some points. The only lines that I am sure run entirely on Metrolink tracks are the San Bernardino-LA and Antelope Valley-LA routes. The others all use UP and/or BNSF tracks at some point. I will admit that the very short Metrolink trains I've seen or been on were on Metrolink tracks. Perhaps they are less concerned than the big freight lines about the shunting issue.

Caltrain is much the same. While it's on its own tracks north of Tamien, it's on UP from there to Gilroy. ACE is almost entirely on UP, except for the last few miles on Caltrain. The only commuter railroad in CA that is entirely on its own tracks is Coaster (San Diego North County).

Aggressive implementation of the axle counts will definitely cause the commuter lines some grief. Most of them simply don't have extra cars (or, in the case of Metrolink, extra cars (non-Rotem) that they are willing to let people ride in) to make up 7-car trains for all push-pull runs. More cabbages would help, since many peak trains are already 6 cars. With Metrolink retiring their oldest F59s, perhaps they might keep some for 6-car trains, or de-motorize them to use as cab cars. Caltrain will certainly have a bunch of F40s available for cabbage conversion once the electrics start running. ACE may be in trouble unless they can find cabbages or junk locos for padding. Then, there's the station platform issue - unless Amtrak long distance stops there, most stations are designed for 5 or 6 cars.

Cal-Amtrak will probably be happy that they bought a couple of trains of Comet cars. Those can be used (after the new cars arrive) to pad out trains for axle count. Are there enough of them, though, to cover all the corridors? Capitol Corridor trains are commonly 20 or 24 axles off-peak (based on hearing detectors on that line at railroadradio.net), and they run a lot of trains; I could easily see a need for CapCorridor to cut back off-peak service in order to have enough cars to pad out all the trains to 7 cars (they're entirely on UP except for the last bit near San Jose).

Back to Cascades: could this provide an excuse for Oregon to abandon service south of Portland? They don't run many trains anyway, and if they have to pad out conventional equipment to 7 cars for all of them they could just say why bother. The rest of the corridor is on BNSF, and their stated axle count wouldn't require many changes once the Talgos are gone.

[conspiracy theory] Are you sure this isn't being encouraged by the Trump Energy and Interior Depts? Dragging 6 or 7 cars around all the time whether or not they're needed for the ridership will require the locomotives to be screaming away all the time in Run 8 burning more fuel than they do now, but reaching lower speeds - up yours West Coast Greenies. Just sayin'. [/conspiracy theory]