The new ebuilds introduced into the main tree from the GNUstep overlay for gnustep-back-*-0.12.0 use the new-style virtual "virtual/gnustep-back", but there is an old-style virtual entry in "profiles/base/virtuals". To prevent a problem with the old versions for GNUstep stuff in the main tree, those should be forward ported to use the new-style virtuals.
The new gnustep packages are stable now, all old packages were removed from the tree. So no more conflict :) Thanks for the report!