Oh Shit, Git!
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Cloning Multiple Repositories
To clone the whole GitHub organization, including wikis or a GitLab group, you can use ghorg
Overriding the Clone Path
To clone in specific directory, you need to set GHORG_ABSOLUTE_PATH_TO_CLONE_TO and GHORG_OUTPUT_DIR in the configuration then the repositories will be cloned under <GHORG_ABSOLUTE_PATH_TO_CLONE_TO>/<GHORG_OUTPUT_DIR>.
Copying a Directory and Its History From One Repository to Another
I managed to get it working with this solution. The accepted answer might also work but I haven't used it.
While they're under the same question, this solution doesn't work because subtree is not suitable for this use-case and the copied commits won't have the proper directory structure in the remote repository and will corrupt the history.