Thanks to everyone for the information. I think the safest thing to do to make sure I make it to my destination is to just keep my butt on the train.
I've just always wondered about how it worked and never could figure it out from the schedule.
You really can't from the schedule, because most stops, even long ones, don't have both arrive and depart times. Also smoking/fresh air stops are subject to operational conditions, so if a train is late, you might not have one that you ordinarily would.
With that said, there are places where you are going to have a relatively long stop no matter how late the train is. Those are service stops and crew change stops. For example, Klamath Falls on the Coast Starlight.
The conductor will typically announce which stops are "fresh air" stops, as they call them now, that you can detrain for a few (or more minutes). The conductor will also usually announce if a stop is NOT a "fresh air" stop and that passengers should not detrain if that is not their stop.
On the Coast Starlight, the "fresh air" stops are Portland, Eugene, Klamath Falls, Sacramento, Emeryville or Oakland (or both), San Luis Obispo and Santa Barbara. Sometimes San Jose. On the Empire Builder, I think they are Spokane, Whitefish, East Glacier, Shelby, Havre, Williston, Minot, Fargo (if you are up), Minneapolis, Red Wing(?), Milwaukee. Not sure of the whole list on the Southwest Chief, but ones that definitely are are Flagstaff, Albuquerque, La Junta, Kansas City. Again, not sure of the whole list on the California Zephyr, but ones that are include Reno, Salt Lake City (again, if you are up), Grand Junction, Denver, Omaha, Ottumwa.
But don't get off at any of them unless the conductor announces you can.