If you specify any "--no-xyz" in PORTAGE_RSYNC_EXTRA_OPTS, then the values in PORTAGE_RSYNC_OPTS will override these settings. So I guess rsync is called with rsync PORTAGE_RSYNC_EXTRA_OPTS PORTAGE_RSYNC_OPTS To my mind it should be rsync PORTAGE_RSYNC_OPTS PORTAGE_RSYNC_EXTRA_OPTS so that you can specifically turn off values (like --no-perms)
Thanks, this is fixed in svn r4659.
This has been released in 2.1.2_pre2-r9.