Fix cross-prefix bugs, and test.

* Fix create_trees to correctly handle the case where ROOT=/ for two
  different EPREFIX offsets.
* For best/has_version, handle the case where ROOT=/ for bug prefixes,
  though each has a different EPREFIX offset.
* Use portage.const.EPREFIX for default EMERGE_LOG_DIR offset, which
  is analogous to existing un-prefixed behavior.
* Use portage.const.EPREFIX for default PORTAGE_CONFIGROOT, which is
  analogous to existing un-prefixed behavior.
* Add cross-prefix cases to emerge tests, including chpathtool for
  binpkgs.