Rule 8.6.2 does indeed say that “The capitals terminator may precede or follow punctuation and other terminators but it is best that indicators and paired characters such as parentheses, square brackets and quotes be nested. That is, close punctuation and indicators in reverse order of opening.” Either way is acceptable. Since you are asking about the NLS/NFB Lesson Manual, however, I suggest you take this up with NFB. You can contact them at transcribers@nfb.org.
Braille on,
Julie