Well yes, since most people don't travel by train anymore, in the interests of saving the taxpayers money (since Amtrak is still gov't subsidized), they are working to alienate and eventually run off the few customers they have left.
The ridiculousness of cycling clothes increase exponentially in relation to the distance from your bicycle.
If I was faced with this, I would look into storing a package the bike would disassemble into so it is luggage. I assume you don't need similar fees and reservations for luggage. A folder would no longer be a bike once folded, but the conductor would likely still toss you, not willing to consider it as no longer being a bike. A box of bike parts is not so obvious if opaque.