When FEATURES=binpkg-multi-instance is enabled, emerge emits warnings for ignored binary packages even though it has selected an alternative binary package with suitable properties. The relevant code is in the depgraph._show_ignored_binaries method, where it should check if selected_pkg is a binary package.
Patch posted for review: https://archives.gentoo.org/gentoo-portage-dev/message/8bed35550319aa09c0579466eb636bcc https://github.com/gentoo/portage/pull/168
This is in the master branch: https://gitweb.gentoo.org/proj/portage.git/commit/?id=0f9bc8659094fe6a100a64e51cc9d51e95c5d659