"But AFAIK is makefile.pl only relevant when installing from CPAN on the client side."
Not necessarily if it's part of the make dist routine. The README will get created inside of the repo, and if the file is already added to git, it'll show up in Github because it's generated prior to creating the tarball. It'll also have to be included in the MANIFEST.
At least that's what I envisioned the desire to be.
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