Simple - the six week challenge you are referring to follows a different set of instructions than the BBB full 3 month challenge, which is what most guys are talking about on here when referencing no extra sets or reps on the big lifts. You follow one or the other, not both.
Since the full 3 month challenge and the six week version are not one in the same, they each have their own sections in the book. For the 3 month challenge done over six weeks, follow what is written in the book.
In the Beyond book, Jim explains exactly why you will NOT go for extra reps on the last set of the big lifts - IF you are following the traditional 3 Month Challenge template.