The FSDO doesn't have wiggle room, they are there to INFORCE the regs NOT help you re-write them to your likeing. The FAA doesn't have local branches set up just so folks can come in and change whatever FAR they don't like and despite what some may think, that's not the job of a POI. He is an INSPECTOR nothing more, nothing less.
No, the NPRM process is in place and a proper chain of command has been established for those who wish to dispute the regs (just ask the folks who are trying to go to age 65, try doing that with just local POI approval) B6 mgt choose to ignore it.
So what FAR was violated? These flights were conducted under Part 121 Supplemental Flight Rules with a relief pilot onboard.