As far as I understood portage configuration is being moved to /etc/portage.
However, portage will complain if /etc/make.profile is missing, even if /etc/portage/make.profile exists. Portage continues to work without any apparent problems, so only the error message is invalid.
!!! /etc/make.profile is not a symlink and will probably prevent most merges.
!!! It should point into a profile within /var/cache/portage/gentoo/profiles/
!!! (You can safely ignore this message when syncing. It's harmless.)
Thanks, this is fixed in git now:
This is fixed in 22.214.171.124 and 2.2_rc84.