Example: in a LDAP setup root user needs /root/.ldaprc for client side certs (they cannot be specified globally). In a LDAP setup recent baselayouts apparently mess with $HOME during startup and services tries to find /.ldaprc instead of /root/.ldaprc. Without that file things like courier-imap, sendmail, openssh with ldap patch and so on will fail to load the proper configuration and require restarting after boot for fixage. Copying (or linking) /root/.ldaprc to / solves the problem but it's certainly ugly.
Using baselayout-1.11.15-r3
should work fine with baselayout-1.12.x imho, putting config files in /root/ for services is stupid in the first place