That seems unrelated, since I have split up my domain into four .conf files and still run into pain.
I have read all of the stuff here and I have only understood half of it or what I understood proved to be no sulution. I am wondering why
./letsencrypt-auto certonly --webroot -w /.../mw -d example.org -d www.example.org
creates the certs without isssues and
./letsencrypt-auto certonly --apache --renew-by-default -d example.org -d www.example.org --dry-run
cheerfully fails. There is something in the water or I am being silly again.