True, the controler should say "altittude" when referring to a hight UNDER the transition layer.
A transition layer is a transition layer so you must stay at 1013/29.92 above it and change to the region QNH as you cross it.
Logic behind it:
Say there is a big difference between QNH and QNE and the controller stopes your descent atFL100, you will have to chenge back to QNE(29.92) and you might forget it aswell and this is no orderly way to conduct a flight.
hope my answer makes any sense.
DT