Folding bike or full-sized bike in a box on Amtrak? It gets even more confusing when your "train" journey is replaced by a bus. This Amtrak station in San Francisco can only be reached by bus, and not all of their buses have a bottom compartment that will fit one of these boxes.
So my choice is: folding bike. The red Bike Friday Air Glide, in particular, which fits into a regular suitcase and can be taken anywhere.