I'm trying to prevent having all the files in root of SD, this was the main point of /homebrew/3ds/.I know what you tried to achieve and I like it. However I have my own path for all application & payloads etc.
I don't like calling it homebrew, so I simply have a folder "3ds_launch" which includes everything that would usually lay around on the root of the SD Card.
And I don't want 2 folders (3ds_launch AND homebrew) if I can prevent it.