I don't know if I understand the problem but here is one data point.
I regularly take Amtrak between San Diego, Ca and Redding, Ca., through the California Central Valley, with my bicycle, both standard and folding, never boxed.
It is a combination of 2 or 3 Thruway buses and one or two trains, depending on how I arrange the trip.
Each time on the bus the drivers require me to slide (and remove) my bicycle into the storage area under the bus.
The driver will not touch your bicycle, it is all on you. But he/she will take care of your luggage.
The San Joaquins train (Bakersfield to Stockton) has a baggage car that you can hand your bare, unboxed, bicycle to store for the trip.
I can start in San Diego @ approximately 4:30 am and end up Redding at about 6 pm, almost 8 hundred miles.
There is a 3 hour layover in Sacramento, but that can be kinda fun as it gives you enough time to bebop around and explore a little on your bicycle.
I don't know how a boxed bike is handled on that particular route but I imagine it would be about the same.
It's a long day but fairly stress free considering I'm taking my bicycle along and not having to box anything.