Wow, deja vu. It's approaching almost 4 years since I first had issues w/ Amtrak and my folding bike and I thought it was all resolved & clear.
In any case, from my own personal experience, NOTHING on the Amtrak web site is real in the eyes of the conductor. It is all about the Operations Manual (Conductor's rulebook), union rules and whatnot.
So read and print out this:
http://community.bikefriday.com/imag...akpolicy07.pdf
And read this story about someone named Dave:
http://community.bikefriday.com/amtrak
Yes, conductors still have final say and discretion so better to be nice to them than argue about the rules.