De acordo com o homem ldap.conf
manpage:
Additional configuration files can be specified using the LDAPCONF and
LDAPRC environment variables. LDAPCONF may be set to the path of a
configuration file. This path can be absolute or relative to the cur‐
rent working directory. The LDAPRC, if defined, should be the basename
of a file in the current working directory or in the user's home direc‐
tory.
então você deve definir diferentes LDACONF
no apache2 envvars
.