We already have this sort of behavior hardcoded for /lib/modules. It would be nice to allow the user to control it with a variable. The documentation should suggest for the user to put the same path in COLLISION_IGNORE when appropriate.
This if fixed in git: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=d1a59831eb2a5205d050884c760cca1d73be8fdf
This is fixed in 2.1.11 and 2.2.0_alpha111.
*** Bug 536216 has been marked as a duplicate of this bug. ***