Please consider renaming it to something else, eg repos.conf.d or repos.d
It can be a flat file or dir, just like most of the rest of /etc/portage/
Ben is correct. It's the same as the package.{use,mask,unmask,keyword} scenario. However, it is (was) undocumented. Fix is in git.
Updated docs: commit http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=69132988b8a9a865d3d46f2c8af1e3f5984c1fc9
Released in sys-apps/portage-2.2.8.