But there isn't any technical reason why you can't just replicate the directoy structure in mfs?

Basically just when you add
dir: test/folder_1
         |-- dir 1
         |-- dir 2
dir: test/folder_2
         |--dir 3
         |--dir 4

It makes it look like this:
/ipfs-sync/
    |--dir 1
    |--dir 2
    |--dir 3
    |--dir 4

Instead of logically expected:
/ipfs-sync/folder_1
                    |--dir 1
                    |--dir 2
/ipfs-sync/folder_2
                    |--dir 3
                    |--dir 4