If you have connections to make, and you're going westbound, that means either SAC to the northbound CS or EMY to the bus to SF.(There mat be other stops with Thruway bus connections too,) in SAC, I think the CZ arrives about 3 pm or so, and the CS departs at midnight, so it would have to be more than 9 hours late to miss it. Besides since it is a guaranteed connection, Amtrak would pay for the hotel cost and get you to your destination.
In EMY (or another stop with dedicated Thruway service), the bus will wait for the train if it's late. Otherwise the bus would leave with -0- passengers aboard and then when the train arrives, they would have to dispatch another bus and driver to the station.