Another minor difference is that if you run a copy, the source and new repositories will have the same parent repository. With the clone, the new parent of the repository will be the original.
i.e. in the [paths] section of your .hg / hgrc file.
Original repository (/ repo / hg / original)
[paths] default = /repo/hg/parent
Copied repository
[paths] default = /repo/hg/parent
Cloned repository
[paths] default = /repo/hg/original
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