Bex
you make a good point regarding the argument that if they stay inside the ATZ, why have a MATZ.
However the nature of the type of flying that is undertaken by the mil is probably enough to warrant a MATZ to afford extra protection to A/C that are often quite a handful to fly and are usually fairly quick, fairly well camouflaged and fairly small (hence difficult to see).
At a busy Mil airfield there is a good argument that the MATZ protects both the transit A/C and the military one. Especially if there happens to be a lot of Mil IFR recoveries happening.
Although it is essentially class G and can be ignored, to do this smacks of very poor airmanship.
MATZ crossings are usually very easy to arrange if you speak to the LARS controller at the airfield, and if someone chooses to fly in the vicinity of such an airfield, they would be reckless and stupid to not at least call LARS for a FIS at the minimum. Mil controllers are on the whole, very good at maintaining an ident even on A/C that are under a FIS (often, they will identify them for their own piece of mind, and will often allocate a squawk, even under a FIS).
I know that you are saying some of your things to continue the discussion and to elicit points of view, so my replies above, are not meant as a reply solely to you, but just my tuppence worth on the subject!
I do think that there are some Mil airfields out there that probably do not require a MATZ status anymore, as they are a lot quieter than they used to be.
If in doubt, always call the unit concerned. Poor flight planning should not occur, even in civil recreational aviation.