I am just thinking about the best way to have everything inside and integrated rather than having bits sticking out 
That was my reasoning behind having a 5.25" or 3.5" bay or two. It would allow users to decide for themselves what they wanted to mount internally or just dangle via the external USB ports.
Personally, I wouldn't mind a real hard drive (2.5" or 3.5") and a DVD+RW mounted internally.
To keep the footprint small, the bays could be located either under or over the FPGA Board.
At the end of the day though, if costs are to be kep to the minimum then I can live without the bays.