As Swanwick isn't an RAF station, why do the RAF there get a flag?
If the Prestwick example is anything to go by, you'll find that the mere presence of the RAF will create an "RAF Swanwick", in much the same way as you have an RAF Prestwick wholly within Atlantic House.
http://en.wikipedia.org/wiki/RAF_Prestwick
The RAF Ensign occupies one of the two flagpoles outside Atlantic House, (the other being presently unoccupied), and a plaque outside the section of the building occupied by the RAF states "Headquarters Royal Air Force Prestwick".
No probs at all with the arrangement here, so can't see why there might be any at Swanwick to be honest.