I have a suggestion of a different way to configure X. I don't know if it's
possible (I think it is) or if someone else has already suggested it (bugzilla
doesn't have something like that at least..). So here goes:
I was thinking about doing the config changes through X instead of regenerating
xorg.conf externally and then restarting the server.
When X loads, it reads the xorg.conf, and in order to change it you communicate
with X.org and tell it what to change\add\remove, X regenerates the config file
by itself (probably making a backup of the old one) and if possible applies the
changes at runtime.
I hope I got myself clear, and sorry if it's already possible somehow.