I'd propose to add an epatch_user call to the sys-apps/portage ebuild, if possible. My current use case is that I wanted to apply an hardened-related patch by blueness for which he asked for testing (commit 9089c2d in portage repo). Granted, I could also have used the -9999 version, but I prefered to only change this detail and stay with my stable portage versions in other respects.
*** This bug has been marked as a duplicate of bug 491256 ***