Since this commit, manifest mode runs QA checks when it should only be generating manifests: https://gitweb.gentoo.org/proj/portage.git/commit/?id=4062c69dc27a816b377b3eb91dcb1c93b6f2cab0 The reason is that the return value from the modules/scan/manifest/manifests.py module's "check" method was being used to control the scanner QA checks loop.
This is in the master branch: https://gitweb.gentoo.org/proj/portage.git/commit/?id=ef33db45a0c1d462411d4ced1857a322c0ab28f6
Fixed in 2.3.0-r1.