Less chance of dust and debris falling between the shutter and the rest of the disk. Plus, that was just naturally the top of the device when you pick it up. It’s easier ergonomics to pick the floppy up from the sides and feed the top into the drive. Also the shutter did stick up a little bit, so if you placed them shutter down they can wobble and buzz in the container with slight vibrations (like say, from a computer sitting next to them). Bottom down makes it more likely that the shutter will get damaged or scoop material into the disk when moving them.

We also just kinda did it that way.