Tucumseh,
The main problem with JSP 553 mixing Airworthiness with the Operational aspects is that it conveniently overlooks the means of rectifying such defects. The budgetary authority to make safety of flight aircraft mods is seldom if ever linked to the budgetary authority to enforce any shortfalls in training, tactics, techniques, and procedures - ie the Operational domain. The net result is 553 implies it has a level of influence and control over the safe operation of aircraft that probably isn't true.
This appears to be a fundamental failure to ensure that MoD policy is underpinned by an effective means of implementation, rather than an unsatisfactory feature of a publication.