You can take Caltrain to San Jose. I did this commute for several years when I lived in SF and worked in SJ. With electrification coming top Caltrain this fall, it should be faster than the current diesel trains. Depending on where Twitter's offices are in Palo Alto and San Jose, it probably won't be that bad.
BART runs with 20 minute headways on longer routes (and as little as 4 minutes through San Francisco). The six CalTrain "baby bullet" express trains run hourly at best, with long service lapses mid-day and in the late evenings. Locals run more often (about every 10--20 minutes during peak commute hours) but add a half-hour to the just over one-hour express schedule.
(Both are still faster by far than driving, particularly during rush hour.)
BART's Green Line (Daly City - Beryessa / North San Jose) departs every 20 minutes from 4:55 am though 7:36 pm (southbound) and 4:59 am through 6:49 pm (northbound):
I commuted for several years to Palo Alto from SF. If you manage to get on a "baby bullet" it was a 37 minute ride, but you also have to get to/from a Caltrain station on each end. In PA, I was lucky that the office was a few minute walk, but in SF it was a taxi or bus ride (this was pre-Uber etc).
As an X employee, if you had optimized your commute around the mid-market area, you could be living less than 45 minutes away on a single mode of public transit, but it could double or triple to commute to the new X offices. Any time you have a transfer with the commuter systems in the Bay Area, it's going to be a clusterfuck from time to time.
Are they upgrading the tracks as well? Diesel trains can run at 80mph no problem, which is about the maximum any standard US railroad supports. If the track is built to high speed standards you could go faster.
Melbourne, Australia has been running a project since 2015 – scheduled to continue until at least 2030 – to remove at-grade intersections (or "level crossings" as we call them) on suburban rail lines. They've already removed 83, and by 2030 plan to have removed 110. I'm not sure of the total cost, but I'd say in the ballpark of US$5-10 billion. The removal is done by a combination of elevating the rail line, trenching the rail line, and leaving the rail line at the same level but building road bridges over it – adopting whichever solution is most feasible and cost-effective for any given at-grade intersection. The project is run and paid for by the state government, with the federal government contributing some of the funding.
Australia's State of Victoria: population close to 7 million, economy almost US$300 billion (Gross State Product), annual state government budget around US$70 billion. California: population close to 40 million, economy almost US$4 trillion (GSP), annual state government budget of almost US$300 billion. If Victoria can afford it, California can too.
