Overlays often have a "soft" policy to have clean CVS header in the ebuilds, that are commited to them. Repoman should have a check to prompt a warning if the CVS header is not clean (e.g. ebuild was copied out of the main tree) and the ebuild gets commited to an overlay (if it is possible to differ between main-tree and overlays inside of repoman). Maybe it is also possible to auto-clean it based on a setting in metadata/layout.conf like "clean_header=1".
Git doesn't make use of the header anymore.