We are assuming that compliance to the service's regulation such as U.S. Air Force Regulations and DoD regulations should equate to compliance to FAR? How has this been accomplished in the past in 3P agreements?
Generally speaking, the DFARS and other components' supplements (AFARS, AFFARS, DLAD, etc.) both implement and supplement the FAR. Implementation involves clarifying the FAR content, while supplementation involves adding content above and beyond the FAR. Then there are the non-acquisition regulations that govern specific programs such as Public-Private Partnerships (P3). These include DOD Instruction 4151.21, “Public-Private Partnerships for Depot-Level Maintenance" and Air Force Instruction 63-101, "Acquisition and Sustainment Life Cycle Management." The latter implements the policy of DODI 4151.21.
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AFI 63-101 clearly states that "Statutory law, Federal, DOD or Joint Staff (JS) directives take precedence" over it. DODI 4151.21 requires the military departments to "Ensure that, in establishing public-private partnerships involving DoD depot-level maintenance activities, such partnerships comply with applicable statutory and regulatory requirements." So it's clear that regulatory requirements in the FAR (which implements federal acquisition law) and its various supplements take precedence over Instructions such as DODI 4151.21 and AFI 63-101. A situation may arise in the planning and operation of a P3 that conforms to an Instruction but contradicts a regulation such as the FAR. That's why the cautionary language exists in the Instructions— to yield to regulations such as the FAR as the tie breaker.