It states that the neck should come with a slight convex box and seems to instruct leveling from that profile. Shouldn’t the neck be completely flat (no bow whatsoever) before levelling frets?
Yes, that is correct. That particular information flow could use a little clarification or re-ordering.

I believe that guide is still a work in progress, or at least a fluid document, and graciously compiled by a Dedicated volunteer. I'm sure it will get sorted in the next release.