I disagree with that recommendation.
There are many cases where you want to allow multiple configurations to co-exist on the same machine. For instance multiple developers on one machine, each with their own home directory. Or staging and production versions of the same site on the same machine, served from different IP addresses.
Of course if this is for broader distribution and not just for internal use, then be nice to administrators and put configuration files where the sysadmin will expect it - namely /etc. But for internal use...?