As an ATC I cannot make any comment on the use of multiple altimeters in aircraft, so, from a controller's perspective, I'm separating my aircraft on the assumption that everyone at or below the Transition Altitude has an altimeter set to QNH, and everyone at or above the Transtion Level have altimeters set to 1013.
I don't care which altimeter you use, as long as when I ask you to report the level you're passing, its based on the correct setting above or below the Transition Layer. That way, when you tell me you're 1000FT apart, YOU ARE 1000FT APART!!!
This is even more critical when 500FT separation is in use. I often correct 300FT variations in Mode C altitude information on radar due to incorrect pressure settings on altimeters.
300FT variation (Aircraft A) + 300FT variation (Aircraft B) = 600FT
500FT Separation Standard minus 600FT total variation =
Remember, my radar cannot measure what altitude or level you're at, only you and your transponder can give me that information...
