/etc/UPower/UPower.conf
takes precedence. Gnome moved from using org.gnome.settings-daemon.plugins.power
for some of the options to this file so UPower.conf is a newer approach.

The file even claims users should not need to edit the file. So if you need to
make changes to /etc/UPower/UPower.conf to make something work do consider this
a bug that needs to be reported as it should affect every user that uses the 
same hardware.