if 2 separate tickets, will delay/missed connection be protected?

[BCL]

Unlike airline tickets, Amtrak tickets hold no value after the train for which they are issued leaves the station. The modification window is extended if the train's departure is delayed, but oftentimes that isn't readily apparent to the agent who might take the call, so call in advance of the scheduled departure. If you receive an agent who can't give you the information you ask for, or is dismissive, or says "there's nothing I can do", politely terminate the call and call back. The odds are pretty good you will get a more helpful agent on the second try (and almost always by the third try). But don't expect them to overturn the laws of physics and make the train go backwards after it has left a station or do other impossible feats (particularly those that may impact their employment status).

Not entirely. There's the option to purchase a flexible fare ticket, and those tickets are 100% fully refundable like a full fare airline ticket. Sometimes I've seen that's the only option for a coach fare. For example, I just checked the CZ for tomorrow from Emeryville to Chicago, and all that's available is flexible at $326. Later days I see the flexible price is the same, but value is maybe $170.
There's also a bit of time (I've heard two hours) to cancel a segment (an receive an E-voucher credit) before being declared a no-show. I wouldn't count on it, but they keep it open some time since occasionally it takes time for a conductor to lift a ticket. If you're really worried about it, having an Amtrak account and a device with internet access will make it easier to modify or cancel a reservation.

On top of that, unreserved trains have tickets that theoretically can be used later for the same station pair, or even cancelled for credit. A few conductors have told me that if they fail to lift my ticket, I should feel free to do what I want with the ticket. Of course that implies a good faith effort to make myself available to have my ticket scanned, so no hiding in the lavatory until arriving at the destination.

That's very interesting and good to know; I speak from my experiences in my first year of Amtrak travel, when I missed the outbound train for an LD trip at the scheduled departure station and when I called about options for rebooking was when I was informed that I should have called prior to the train departure time. The second time was when I was departing PHL for CHI via WAS and missed the outbound Northeast Regional. I knew that the next (and last) option was to catch the Acela, so I showed up at 30th Street Station and requested to be rebooked. I had to pay $130, which I thought was full fare value at the time; but perhaps that reflected a trade-in value.
Both of these were in the days of paper tickets and I don't recall seeing three tiers of fares then as I do today. Since the advent of eTicketing, I've had fewer issues with rebooking (and sometimes purchase a backup ticket when my plans are uncertain since I know I can receive full value). I've also since booked a last-minute ticket via telephone agent and been told that my "Saver" fare was fully refundable. (Even though I had no worries since I was already at the departure station and then the ticket was only around $39, so any loss would have been minimal.)

Flexible is new. No-shows in the past still held their value towards a voucher.

 

[BCL]

That's very interesting and good to know; I speak from my experiences in my first year of Amtrak travel, when I missed the outbound train for an LD trip at the scheduled departure station and when I called about options for rebooking was when I was informed that I should have called prior to the train departure time. The second time was when I was departing PHL for CHI via WAS and missed the outbound Northeast Regional. I knew that the next (and last) option was to catch the Acela, so I showed up at 30th Street Station and requested to be rebooked. I had to pay $130, which I thought was full fare value at the time; but perhaps that reflected a trade-in value.

Just thinking of it in terms of what's possible vs what a human agent thinks is possible. The issue with calling up and speaking to a person is the wait time and the possibility of something being misunderstood over the phone. If you can modify or cancel, those options should be available to you via one of Amtrak's electronic interfaces. I've actually cancelled a reservation at a Quik-Trak kiosk before, although I could have done it online. If it's possible, the computer isn't going to tell you it's not.

If you were going way back to paper tickets, you always had the option of just failing to show and requesting a voucher or asking for a refund minus the penalty.