QNE is not an altimeter setting, it is the indication on the altimeter when landing at an aerodrome with the Standard Pressure Setting set on the sub scale. It is used at high altitude airports where QFE is too low to be set on the sub scale. QNE has nothing whatever to do with 'Altitude above MSL', it is not 'used when above 3000ft' or 'only if dealing with ATC'.
Thanks BillieBob
Question; you have to set 1013.2 on the sub scale so surely this is a setting procedure? What I meant by 3000ft was the UK's transition altitude to use QNE over QNH.