Good post Paul, this is the sort of thing everyone new to collecting should read. I'll add that, as Kirill Rivkin points out, even if the certifying body does everything right, a dishonest seller can find a way to attach good papers to a different sword:
http://historyswords.com/2018/10/23/kiyomaro-modern-papers-and-100-guarantee/
As you say, the only real defense against this on a personal level is by educating yourself on the subject. I will add that we're blessed to have a lot of educational material available to us, as well as expert individuals and organizations that are willing to give their opnion, both of which help us to properly identify a sword. But, the only way to keep them is to keep supporting them. In other words, keep buying/reading/critiquing those books, keep renewing those memberships, keep looking for opportunities to see real swords up-close, and most importantly, do whatever you can to spread the knowledge and appreciation of the Japanese sword.
And, not to derail the thread, but if you're someone that doesn't believe that a large, prestigious certifying body full of experts can't get it wrong, remember that the FAA certified the 737 MAX as airworthy!