You could probably do it, but I wouldn't suggest it. If something goes wrong while updating the factory reset firmware, it would be difficult to remedy (especially on models that lack an internal uSD card).

If you're concerned about the update process because you have a slow internet connection, you could always download the firmware once then apply the update manually after doing a factory reset.

(If you want to do so, it looks like the factory firmware is kept on a separate partition and is copied over when necessary. You should be able to extract KoboRoot.tgz into the root directory of that partition, but I'm making no guarantees.)