This comes from here.
Since it is an upstream issue, I am reporting it here.

This file contents trigger the notice there must be exactly one blank line after the file comment
(note that there is a blank line after the comment, and even if adding more than one blank line won't change this message)

<?php /** * Intentionally empty file. * * It exists to stop directory listings on poorly configured servers. * * @package whatever */ 

This does not trigger that warning:
(note that the only difference is we added something after the blank line after comment)

<?php /** * Intentionally empty file. * * It exists to stop directory listings on poorly configured servers. * * @package whatever */ echo 'this'; 

I don't think it is OK to assume there will be code in any case in a file, even when there is a comment.
Thus, the warning is faulty and should probably only trigger if there is really no empty line after comment, which is clearly not the case here.