I will be taking Amtrak in June but because of Covid they have made changes that make it more difficult to bring my bike. I will be traveling through Portland, OR to get to Whitefish, MT. The train to Whitefish from Portland no longer provides bike service so I will have to box my bike.
When you say "no longer provides bike service", do you mean roll-on (unboxed) bike service? If so, the Empire Builder from Portland to Spokane never offered this.
When Amtrak started to do roll-on service on the Empire Builder a few years back, they only did it for the Seattle segment.
Under the category of what goes around comes around, I'll point out that my first big cross country trip included a ride in May of 1979 from Chicago to Seattle on the North Coast Hiawatha (with a layover week of training in Missoula) and then down the coast to LA. (FWIW, '79 was the last year for the Hiawatha, hitting the Congressional cutting block in October.)
I rolled my fully loaded Bob Jackson crit bike (Messina) over to the baggage car at Union Station where a Greek-American baggage handler rolled it onto the baggage car and secured it. Rolled it off and on in Missoula and Seattle, and off in LA. Worked like a charm, and the tips didn't seem mandatory. I suspect that with fewer personnel, less care in loading, and more complaints of damaged equipment from cyclists, the move to mandatory boxing followed.