Question is why the /etc/openldap/slapd.d file structure is there for users to edit in the first place? Wouldn't it be even more misleading if the running one is modified on the fly while the one in slapd.d/ is not? A bunch of online tutorials and howtos are actually asking people to touch those files, such as cn=config file at least for initial setup.
The OpenLDAP project has no control over how Linux distributions decide to deploy their configurations, or any control over online tutorials or how-NOT-to's. Feel free to file bugs with Debian, etc, to fix their cn=config layout. Feel free to email people who have posted online tutorials and how-NOT-tos to either correct them or take them offline.
--Quanah -- Quanah Gibson-Mount Sr. Member of Technical Staff Zimbra, Inc A Division of VMware, Inc. -------------------- Zimbra :: the leader in open source messaging and collaboration