Great question(s). A phone call with the question submitter revealed some other details.

Bottomline is “yes”. If you have mandatory clauses that need to be included in the NASA SEWP Order because of your Agency’s policy; they should be included in the RFQ or FOPR. The FAQ page on NASA SEWP does specify Agencies ordering off them need to follow Agency rules and the Vendors of the GWACs do understand that.

From the NASA SEWP site (Ordering):

The internal ordering process of each agency varies. The process and accompanying forms for PR's and DO's that are issued against a SEWP contract is defined by the issuing agency and not the NASA SEWP Program Management Office (PMO). The typical process, however, is for an end-user to determine a requirement and generate a purchase request (PR). The PR along with any necessary funding information is sent to that Agency's procurement office which results in the issuance of a delivery order (DO). Any valid Federal Agency DO form and the associated delivery order number may be used. The NASA SEWP Program Management Office (PMO) does not issue DO's - these must be issued through the issuing Agency's procurement office. The SEWP Program Management Office (PMO) reviews, processes and tracks issued DOs and forwards them to the Contract Holder(s)

Some agencies have special requirements for issuing IT Delivery Orders. It is the Issuing Agency's Contracting Officers' (COs/KOs) responsibility to be aware of any agency-specific policies regarding issuing orders via an existing contract vehicle and Government Wide Acquisition Contracts. There are no requirements under the SEWP Contracts for issuing agencies to use other intermediary procurement offices, except as directed through their own internal policies. Some agencies have special requirements for issuing IT Delivery Orders. It is the Issuing Agency's Contracting Officers' (COs/KOs) responsibility to be aware of any agency-specific policies regarding issuing orders via an existing contract vehicle and Government Wide Acquisition Contracts.