Sounds like it might speed loading and unloading, but does it? Getting a bike from one end of the car to the other, in the narrow aisle between seats, is pretty tricky--especially on a crowded moving train!
I think conductors have decided this is a bad idea since they never seem to enforce it.
It might actually work if the cars' interior layout were rearranged a bit--make one side of the lower level just for bikes, and the other just for seats. I hear that other operators that use these cars (like ACE) do have different layouts, though I haven't seen this myself (but they still impose the stupid 16 bike limit, which is apparently mandated by the feds).