If I recall correctly, there is a general ANO provision that military aircraft are to be operated in accordance with whatever JSP318 is called these days rather than in accordance with the ANO. Check the FPD for clarification of the 250 below 10 exemption in UK airspace.
The Rule 5 500ft rule refers to 'people, vehicles, vessels and structures' rather than a 500ft MSD. So you can legally go down to 1 molecule MSD in a civil a/c so long as there aren't any people, vehicles, vessels or structures within 500ft.
Have been away for a couple of weeks checking car parks, hence the absence from PPRuNe.