I was wondering why /usr/local/etc isn’t used for storing local changes to system-wide configuration (which is in /etc/). Even after quickly reading through FHS’s definition for the contents of it, “Host-specific system configuration for local binaries”, I was convinced that the practice of adding local customizations directly to /etc must be flawed.
It was only after re-reading the definition with thought when the emphasis dawned on me: it is used for configuration of local binaries, not for local configuration of binaries.