Commit in question is https://github.com/gentoo/portage/commit/3cd8cf93abb6410cc877381531bb662a704dffa7.
It changed syncing method for git from pull to fetch+merge making sync-git-pull-extra-opts unusable since options like --rebase or --ff-only aren't recognizable by either fetch or merge or both. `sudo -u portage git config --global merge.ff only` might help as an alternative to --ff-only but not with rebase. --ff-only is actually just an example and is useless in my case.
I suggest if this method isn't going to change, just drop the sync-git-pull-extra-opts option and probably add sync-git-fetch-extra-opts and sync-git-merge-extra-opts, even just for the sake of consistency.
Maybe also allow something like sync-git-merge-method = rebase and add sync-git-rebase-extra-opts option so git-rebase is used instead of merge, but that's another feature request to make. But first drop sync-git-pull-extra-opts so people stops trying to rely on it.