Rob
I'm not sure where you found that JB has the signature in a different place. As you say, they are all obverse D (Freeman 2).
I agree about the Je to Jk repairs. I'm assuming that collectors have sent in photos of these repairs to Michael who decided to include them, purely for illustration. The list of die repairs is virtually endless and I personally don't regard them as particularly noteworthy, other than the occasional spectacular example, e.g. N over Z, E over P etc.
Clearly, these repairs are of interest to some collectors, viz Larry's numerous examples of similar repairs on halfpennies on this Forum.