I don't see what would prevent Amtrak from being able to use cars similar to NJT Multilevels as an Amfleet replacement. NJT's former ACES service used them in an intercity configuration, so why not just copy that configuration and use it on Amtrak. To make up for the lack of luggage space, they removed a couple rows of seats and added a luggage rack. Also, there would be no need for the quarter point doors, so that space could be used for more seats or luggage space.
For the cafe cars, the design would be more complicated. I thought it would work well if cars were built with the cafe on the lower level and regular seats on the upper level. However, the raised floors where the seats are on the lower level could pose a problem. I'm not sure if the raised floors could be removed without changing the structure of the car significantly. I believe ACES had the bar on the mid level at the end of the car. That could work with the cafe on the mid level and booth style seating on the lower level (like the Amfleets) with regular coach seating on the upper level. That way people who wanted easy access to the cafe could sit in the same car, if they didn't mind the increased traffic and noise.
