If you are going to wed the motherboard to the expansion board, why not go with the Apple II layout and put it all into a single case with the power supply, keyboard and MB/Expansion in a single chassis. If you look at the 1450XLD as an example, you can have a very Atari-like design that can support a monitor on top with minimal bulk.
But, skip the internal FDD. A flash-drive that plugs into a card on the expansion bus (ie Side cart) makes much more sense to me. i suppose a single Disk Drive to support the Atari/CPM system could be considered but is it necessary? Again, the Apple II with its external drives could be an option, but I wouldn't think stacking them above the computer and under the monitor would work as well.
ETA - there's still the SIO port for external drives.