I guess it's how you define MOD? Ordnance factories and storage, or Military Railways as a whole, or how about the Forestry railways?
The main Naval Dockyards and depot railways were mainly in built up areas to give those who would like to model buildings and produce an almost narrow gauge 'warren' model, however there were several depots used for munitions spread around the country and at smaller ports.
There were the RAF and Army camp railways which are probably better known, Longmoor, Catterick, etc. But how about the RAF's Calshott Spit narrow gauge?
A rural scene could be created based on the Cleobury Mortimer and Ditton Priors, or the Shropshire and Montomeryshire, or even the little Acorn Patch Depot in the Forest of Dean as used by the US forces during WW2, (Lots of trees required!) Not forgetting the 'Secret Factories' with their own terminii.
The railways of the MOD / WD / RAF and RN were as varied as the locomotives and stock used on them, covering a multitude of uses, it doesn't all need to be big loops....
If ever there was an ideal for Rule One then MOD railways probably fit it.
There was an article in the Southern Way Issue 10 which had a good selection of Porton pictures and plans.