Section 3 and Section 4 are aligned closely (both are entries in the dataRequirement section of the JSON), but the text doesn't make the alignment or differences between them clear.
There should be something that says:
All retrieves are included in the dataRequirement section.
Retreives include the information for their corresponding value sets and direct reference codes
Any direct reference codes or value sets not referenced by a retrieve will be included in dataRequirements using an element of type "CodeableConcept".

This is kind of there already, but not laid out all in one place. Some text like this would clarify things.

It may also be worth considering putting section 4 ahead of section 3, or combining the two sections to increase clarity.