Calling emerge with --configroot set, I still get:
Autounmask changes successfully written.
Would you like to add these changes to your config files? [Yes/No]
* IMPORTANT: config file '/etc/portage/package.use/xtables-addons' needs updating.
(we should also get rid of this let's-just-append-stuff-to-some-file logic)
Please post your emerge --info
If you also use --root, then /etc/portage is used for build-time dependencies from DEPEND. Did you use --root or ROOT?