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MATS pt1 states that aircraft inside controlled airspace are deemed separated from unknowns outside, however the controller is told to aim to keep at least two miles within the boundary-to take into account 'unpredictable' manoeuvers.
There may be local differences to this-at our unit we have slight differences in our local orders-but by and large thats how we carry on. Yes you are quite right when you state that if you are under a stub for instance you may be only 600ft below the IFR traffic-this is something that happens a lot under our eastern stub, where the base is 1500ft, but by and large is not a problem-this situation is a fact of life under the london TMA, as my previous existance working at an airfield to the west of stansted showed!
On a personal note I much prefer to be working the traffic thats near the boundary, you may well not get a radar service-but just identifying you can help a lot, again this is not always an option to my busier colleagues down south-please do not be put off calling a unit even if you dont intend to transit the airspace concerned but are flying close to them (no doubt this will set the cat amongst the pigeons with some controllers!)