SpannerSpinner, are you absolutely sure about what you post. The Air Systems Group (formerly ADRP) changed some fairly key definitions in the JSP553 last year, and many people were not happy with the changes I don't have a copy to hand, but they changed the way they refer to designer, design organisation, design authority etc. I don't know if it's been changed back.
They made changes such that the IPT is regarded as the Design Authority, in the sense that they have the ultimate authority over the design of an aircraft. The designer or design organisation can make recommendations, but the IPT can go it's own way. This would obviously be a move that would be fraught with risk, and would take some justification, but it reflects the legal situation. You can't get away from the fact that the MoD owns the aircraft, maintains and operates the aircraft and is also the regulator. So using your strange analogy of judge and jury, yes the MoD is ! Does it all lie within the IPT, good question. IPTL signs the MAR, RTSA looks after the RTS, but look at the size of the IPT and its resources, then look at the RTSA, and you'll see who's really making the decisions.
The front of the JSP553 contains a statement from the SofS for Defence, it states that the MoD will regulate it's aircraft such that airworthiness is maintained to as standard which is at least as good as the civil world. Think about that statement and its implications very carefully. I wonder if anyone could ever show a conflict of interests: owner v operator v regulator ?
S_H