I've just hit the same issue - I was wondering why I couldn't shut down or restart the service!

In looking at how to fix it I see that /lib/init/init-d-script will call a do_start_prepare function if defined, so I've edited /etc/init.d/uwsgi-emperor to add this towards the end to pre-create the pidfile (as uwsgi will just write to it if it exists):

do_start_prepare() {
        # Create with correct permissions in advance as uwsgi with --daemonize creates it world write otherwise
        touch "$PIDFILE"
}

That seems to do the job (dunno if it's worth/problematic to set umask explicitly in the init.d script as well to ensure that pidfile is correctly created).

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