I have to say my own experience is different, but then my experience was primarily with the Harrier II and stopped when it left RAF service (December 2010). At that stage the MAA regime was still "work in progress" in many areas. But on the harrier platform we had a full safety case with supporting evidence that went through MAR Recs into the RTS production, and the arguments were traceable to specific features of the design & operating context. A major part of the GR9/9A/T12 upgrade was ensuring the validity of the safety case remained for the new configuration. But to do it we had a team of specialist system safety engineers, and they spent weeks working in collaboration with Harrier IPT specialists to ensure there was a common understanding of the safety case as written.
If you know of this company you'll also know that at that time each aircraft project was a separate "sovereign entity" with its own procedures and approaches, so I have no idea what they did on the Hawk projects.
Actually I was pleasantly surprised that three engineers only gave rise to three opinions - normally I'd have expected at least five...
PDR