I've been on three train trips of over 24 hours, as well as a few shorter trips, and I've never been delayed by more than an hour. I've heard some horror stories, but trains do run on time more often than not.
But yes, this specific train does require that all bikes be boxed.
Although I did meet a couple of guys that took a train from Cincinnati to West Glacier with their bikes and touring equipment stowed in big hockey gear bags, thus avoiding the additional bike box fee.