The connection is protected. But that does not mean the train will be held, it means that they'll take care of you and see that you get to your ticketed destination. They'll generally hold the Builder for up to about 30 minutes for the Starlight. This is more than it seems, since there is a pretty generous pad between Salem and Portland, about 20-25 minutes, IIRC. If it is severely delayed in California, so it won't make it, they'll generally do Klamath Falls-Pasco bus bridge.