While the instructions, evaluation criteria, and statement of work contain most of the requirements that the customer expects you to address, there may be other requirements in other sections of the RFP that need to be part of the proposal. There is no way to avoid it; you have to read the whole RFP in order to make sure that you have accounted for all of the requirements. Significant terms, conditions, and requirements that impact what you say in the proposal can hide in any section of the RFP and are sometimes mislabeled.
The fourth step in building a compliance matrix is to incorporate any requirements from other sections. Do this by taking the foundation created in the first three steps, and then adding headings if needed to address the other requirements.
If there is no logical place in your current outline to address the other requirements, then you need to create a place for them. For each item you add to the outline, make sure that you identify the RFP reference that drove it to be added. In order to demonstrate compliance with the RFP, you should make sure that all of the RFP requirements are accounted for in the Compliance Matrix.
If the RFP includes a narrative description of the requirements, then you will need to decide whether to add new headings or add notes to make sure that your proposal is fully compliant.