If I do something like PORTAGE_CONFIGROOT=/sub ROOT=/sub emerge -avtD python, it tries to replace the python in the live system. This is a regression in the trunk (5088) since 2.1.1-r2. This seems to happen when a circular dependancy into the live system reaches an ebuild specified for the target system on the command line.
Thanks, this is fixed in svn r5105.
This has been released in 2.1.2_rc2-r1. Your make.conf/ROOT and --config-root features are also in there.