If you're using Slackware, or another sane distribution, /etc/X11/xorg.conf.d/ is where you put user-specific X configuration. Making the config immutable would prevent overwrite.

Making local edits in any part of /usr/ is extremely frowned upon.

Apologies. I haven't been using Ubuntu in a while and did not know you had to modify stuff under /usr there. (Eww!)