xorg.conf and other files are copied into the build in src_install(). If a package is built on machine 1 and installed on machine 2, this will result in the conf file being updated, then transferred from 1 to 2, rather than the one from 2 being updated. The goal is to do this updating in a way that allows etc-update to be used to merge the new changes. Therefore, it needs to be done in or prior to src_install(). The only function relevant only to the install machine that meets those conditions is pkg_setup(). (Although that may not even be run for binary installs -- see http://bugs.gentoo.org/show_bug.cgi?id=58526#c19 and http://bugs.gentoo.org/show_bug.cgi?id=25152.) For this to work optimally, pkg_setup() MUST be run for binary installs. Other options include: 1) Hacking it directly on the live filesystem, without allowing etc-update. This sucks because it takes the choice away from the user. 2) Not hacking it at all and just having some einfo. This will break people's systems if they don't read einfo (which, of course, everyone reads).
Also, note that a sed into ._cfg0001_xorg.conf and friends is broken. This assumes the user always runs etc-update so cfg000{2,3,...} don't exist. If this needs to be done, the filesystem will have to be checked for the highest number in the cfgXXXX, then add a new file one higher.
Fixed in 6.7.99.902