HEDP,
I speak as a pilot of large jets, so please forgive my perspective as I very rarely operate VFR.
I don't understand what you mean by saying that there is more heads-in checking of plates when operating on QNH. The cleared altitudes are flown and the procedure followed until visual or at DA. The only extra work is to make a mental note of the airfield elevation at briefing stage - so that correct height for range judgement can be made once visual. In return for that one calculation you can have a warm feeling of knowing exactly how high you are above the terrain whilst IMC. Having experienced some appalling ATC around the world I am glad that they were not using QFE - which would have left me with a much more difficult task of trying to maintain awareness of "I'm that high above the airfield, so where does that put me relative to the mountain". Hence I am not quite so trusting of terrain clearance being left to correct procedural interpretation by a person on the ground. Perhaps your different view comes from VFR ops, where you are usually in sight of the ground?
In my experience UK deployed ops take place on QNH in accordance with host nation AIP. Even where we provide the ATC we usually share the airfield with the Americans and our own charter flights, both of which will operate on QNH. Traffic on different pressure settings always seems like a bad idea.
I disagree that Kinloss/Lossie is a red herring. There are many TMAs/CTZs in the world that serve multiple airports in close proximity and operate a common altimeter/QNH. The barometric pressure in the zone will be the same, and the precise pressure at each TDZ is not required and the differences in elevation are taken care of by having discrete DAs. There are no height errors as everybody is using altitude. Take the case of parallel runways - either you have a seperate QFE for each runway or operate on the same QNH with different DAs - each of which give the required OCH. Kinloss clutch procedures are based on Lossiemouth QFE, so an aircraft at DH at Kinloss is referencing the precise pressure at a TDZ several miles away! Yes, these procedures are workable, but the degree of reverse-engineering required highlights the anachronistic nature of QFE ops - why not just use QNH like the rest of the world?
The UK military operates several ATC procedures that are at odds with worldwide practice. Each can be justified on an individual basis, but net consequence is an unnecessary lack-of-commonality which, in my view, actually reduces the safety margins. As we concentrate our remaining forces on fewer bases the number of MATZ has been reduced, but traffic around those that remain has increased. Perhaps it's time to make a case for giving the bigger bases proper Class D CTZs? Transiting civilian traffic could not then ignore the airspace. In return the military could offer to standardize it's practices with ICAO/JAR to allow civilian traffic to use these zones more comfortably.