Of course there is a major difference. Just as their is a major difference between most Southern Baptist Churches and Westboro Baptist Church.Notice you highlighted one part with "LDS" and another with "FLDS". I would suspect there is a major differrence in the 2 groups.
However, in Under the Banner of Heaven, as well as your post, the author tries to blur that major difference, basically stating that becoming a member of the FLDS is a very natural movement for those who are devout members of the CoJCoLDS.