Comment # 3 on bug 1232669 from Thorsten Kukuk

That code is just wrong, somebody has no clue.
The config search path on all this distros is the same: look in /etc/pam.d, and
if there is no file, look in /usr/lib/pam.d.
If you want to modify that config:
If there is no file in /etc/pam.d,copy that from /usr/lib/pam.d to /etc/pam.d
and modify it there.
This is upstream behavior and not configurable by distributions. Even if a
distribution does not use /usr/lib/pam.d by default: a third party application
can use it.
And if gdm-config can not handle this correct the code is broken by design and
the author should start reading manual pages.