Trim Stab,
As UK military pilots also do not study the same theory as civil pilots how could the MOD argue to EASA that the qualifications conform to the same standards?
Very easily! The military pilots that operate the aircraft that you hint at, do indeed study the subjects that you talk about. They have to - it's their business. Indeed, they routinely have to go into detail that many civilian pilots wouldn't have come across since their training days; for example, the level of ops support provided to a military pilot on a one-off flight to somewhere in Africa isn't a patch on what BA pilots would get flying from London to New York - so they are often on their own to do trim sheets, perf A calculations, aircraft turn-rounds, flight plans and the whole range of other things required, from scratch, to keep the show on the road.
As regards the choice of diversion airfields and weather factors; again, the rules that govern military crews in peacetime are now all but identical to civilian regulations. Even ETOPS considerations are on the way for some crews. So you see, there really is little difference for the military crews that we're talking about.
Admittedly, fast-jet pilots will need to study some new subjects, that weren't previously relevant to them, before they move across to flying the big kit in the environment that we're talking about; but my experience is that they learn quickly.