Removing default setting from portage itself causes any system that does not use a portage tree to ignore config protection and any other sane defaults. BINHOSTs use binaries directly the same way GRP does, ignoring the tree, using it if available as SUPPLEMENTAL data.
Fixed on or before 2.0.51.22-r1
Looking through the batch of bugs, I'm not sure that some of these are actually fixed in stable. Others, the requirements have possibly changed after the initial fix was committed. If you think this bug has been closed incorrectly, please reopen or ask that it be reopened.