I do think the main reason for the issues is lack of experience (and even someone riding for years can lack an experience dealing with the problem horse). The "no bond/relationship" usually just a consequence of it (although there are exceptions too). And "bad experience in past" is an icing on cake.
Interesting article. Although from what I read/experienced "Thinking like an horse" is a baseline almost every NH trainer says and tries to teach/explain to the students. Whether it's PP, CC, Stacy, Ray or pretty much anyone else I know of.