Since bug 586410, it's possible for FEATURES=unmerge-backup to overwrite binary packages that don't correspond to the installed instances. This behavior should be documented, and there should be a suggestion to enable FEATURES=binpkg-multi-instance.
The existing behavior can be very confusing if the user installs a binary package which is then overwritten by FEATURES=unmerge-backup. In this case, the user could run `emerge --usepkgonly package` repeatedly, and end up alternating between two different builds of the same package version.