- How does one activate the deployed product if extlinux is the active bootloader? The website has only instructions for GRUB (bls_import, etc).

Ah, you probably hit this:
https://bugzilla.gnome.org/show_bug.cgi?id=726007
This is also related:
https://bugzilla.gnome.org/show_bug.cgi?id=722845

Basically to make ostree drive extlinux, the layout needs to look like this:
https://github.com/cgwalters/rpm-ostree/blob/master/src/autobuilder/js/libqa.js#L359

- How does one get rid of the 'traditional Fedora' once the product is active?

Maybe something like:
rpm -qal | while read line; do rm $line || rmdir $line; done
rpm -qal | while read line; do rm $line || rmdir $line; done

...figure both won't be necessary anymore once we can use Anaconda to install a product directly, but in the meantime it would be helpful for some testing and more generally help my understanding. :)

Yep, Anaconda support will fix both.