Not only I don't see benefits (not even for power users, since those will repartition/remove the FAT32 partition entirely either way)
but I see added complexity -- since any modification to the default system scripts would need to handle units with the older layout.
In fact, ANY modification to the currently relatively understood simple system will probably make it harder for people to create their custom layouts, unless it's specifically directed to simplifying it - like for example removing the autogenerated fstab nonsense.
hildonfm is opensource; you can edit it and name the folders per your liking.