E/M Documentation Clarification Needed


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In the "Medicare Physician Guide: A Resource for Residents, Practicing Physicians, and Other Health Care Professionals" on page 121 the requirements for a Comprehensive Examination states "should include at least nine organ systems or body areas. For each system/area selected, all elements of the examination identified by a bullet should be performed, UNLESS SPECIFIC DIRECTIONS LIMIT THE CONTENT OF THE EXAMINATION. For each area/system, documentation of at least two elements identified by a bullet is expected."

My question is what exactly is meant by "unless specific directions limit the content of the examination" and how should it be applied?
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These are the 97 Documentation Guidelines for the multi-system exam. See below where there are areas giving the examiner minimal requirements. In the lymphatic system, the instructions say:

Palpation of lymph nodes in two or more areas:
C Neck
C Axillae
C Groin
C Other

and in Musculoskeletal System, the examiner has the option of:

Examination of joints, bones and muscles of one or more of the following six areas: 1) head
and neck; 2) spine, ribs and pelvis; 3) right upper extremity; 4) left upper extremity; 5) right
lower extremity; and 6) left lower extremity. The examination of a given area includes:

And in Genitourinary, you have a male/female option.