Interesting article, and I feel that it's pretty fair. At first, I thought they were talking about this checklist, but I see they're different. The version I followed doesn't seem to have the same issues (lists jurisdiction but doesn't give it a rating, doesn't list or rate encryption methods at all, no summary at the beginning, etc.).
I think checklists/matrices still have their place, as listing all the branches/options might get too cluttered for a diagram, but I do understand why flowcharts (or the neat venn diagrams that get posted here often) can express information better. I don't think checklists are inherently biased, I just think you need a good decision maker behind the list.