The files c_config.xml, global_prefs_override.xml, gui_rpc_auth.cfg, and remote_hosts.cfg are configuration files which the user can edit (even if most won't), so Debian requires that they be under /etc,
while the "usual" place for them is the working directory. Right now the Debian package takes care of this with soft links. A more robust solution would be to have the core client look for the files in a list of places, using the first it finds. The files in the working directory would be checked first, and used if they exist. The files in /etc/boinc would be checked and used if nothing is found in the working directory.
See the discusion at http://boinc.berkeley.edu/trac/wiki/UnixClientPackage