In GLEP 60, MISC manifest entries inherit from the abstract _INFO type, which is defined as follows: _INFO (new, abstract) This is the functionality of the old AUX, but does not include the implicit 'files/' prefix in the path, and is verified relative to the working directory instead of $FILESDIR. The modification or absence of a file listed as a _INFO-derived type is not an error unless the package manager is attempting to be strict. We can add a repos.conf setting to control this strict behavior (the [DEFAULT] section can be used for global settings).
I've posted a patch for review: https://archives.gentoo.org/gentoo-portage-dev/message/e2641fb28432d76f630f2c139e096852 https://github.com/gentoo/portage/pull/71
This is in the master branch: https://gitweb.gentoo.org/proj/portage.git/commit/?id=f8b1d840de9ffd9aa86dc8666d8915826ffa0f63
Fixed in portage-2.3.3.