Al menos en mi sistema (OS X 10.9.2), veo que el apache se va a utilizar /private/etc/apache2. Nota SERVER_CONFIG_FILE
a continuación:
$ sudo /usr/sbin/apachectl -V
Server version: Apache/2.2.26 (Unix)
Server built: Dec 10 2013 22:09:38
Server's Module Magic Number: 20051115:33
Server loaded: APR 1.4.5, APR-Util 1.3.12
Compiled using: APR 1.4.5, APR-Util 1.3.12
Architecture: 64-bit
Server MPM: Prefork
threaded: no
forked: yes (variable process count)
Server compiled with....
-D APACHE_MPM_DIR="server/mpm/prefork"
-D APR_HAS_SENDFILE
-D APR_HAS_MMAP
-D APR_HAVE_IPV6 (IPv4-mapped addresses enabled)
-D APR_USE_FLOCK_SERIALIZE
-D APR_USE_PTHREAD_SERIALIZE
-D SINGLE_LISTEN_UNSERIALIZED_ACCEPT
-D APR_HAS_OTHER_CHILD
-D AP_HAVE_RELIABLE_PIPED_LOGS
-D DYNAMIC_MODULE_LIMIT=128
-D HTTPD_ROOT="/usr"
-D SUEXEC_BIN="/usr/bin/suexec"
-D DEFAULT_PIDLOG="/private/var/run/httpd.pid"
-D DEFAULT_SCOREBOARD="logs/apache_runtime_status"
-D DEFAULT_LOCKFILE="/private/var/run/accept.lock"
-D DEFAULT_ERRORLOG="logs/error_log"
-D AP_TYPES_CONFIG_FILE="/private/etc/apache2/mime.types"
-D SERVER_CONFIG_FILE="/private/etc/apache2/httpd.conf"
Normalmente /etc es un enlace simbólico a /private/etc, pero si no está en su sistema, lo que puede explicar la discrepancia.