The only racks I can imagine anyone having to remove would be wide Porteur style racks. Even with a 22 inch framed bike with long chainstays I didn't have to remove either of my racks. Unlike the bike boxes that I remember being delivered to LBS, the Amtrak box doesn't require you removing the front wheel. I had actually begged one of those plastic drop-out protectors from my LBS before I used Amtrak but didn't end up needing it because I was pleasantly surprised to find I didn't have to remove the front wheel.
The handlebars on the other hand - I did end up leaving them dangling by their cables/draped over the top tube because it didn't seem to fit in the box just turning them sideways, but I have a high stem, riser bars, and bar ends. I would've liked to have seen the expression on my face when the guy took my bike box from me and casually up-ended it onto it's rear and started dragging it away though! I probably audibly gulped and my eyes where probably huge too! I wasn't expecting that, I might have secured the handlebars to the TT and padded the frame from my stem/handlebars with a cloth if I had realized the box was going to be treated that way!
What I'm wondering is: if I go to folding pedals will they be slim enough folded that I won't have to remove them - given the fact I also have pedal extenders on.
I don't have this brand, but the pic here illustrates the extra width this adds:
http://www.bikescor.com/product/knee.htm