I was pretty confused about how the various mk.conf and extra.mk.conf files would come together. (And the bootstrap /usr/pkg/etc/mk.conf would have blown away my /etc/mk.conf if I hadn't already deleted /usr/pkg before extracting it [because of my symlink].) I don't think the post nor the docs really explain it well. I think it would help for you to just say "nearly everything you usually put in /etc/mk.conf should go in extra.mk.conf, except A, B, C".
As raised in my first comment to your blog post: