Is it possible that the transponder reports an altitude from a selected altimeter system?
It better not, because ATC radar will apply a correction assuming it is sending reference 1013.2. Our QNH setting usually comes digitally from the Met, but we enter it manually in bypass mode. If you change the QNH setting on the console in this mode you can see the levels on aircraft operating at altitudes change, not those at flight levels.
Believe you are wrong, but I had held a radar rating (high level sector) for a number of years with the same wrong idea so don't feel bad.
Back to the original question, if I instruct you to descend to 9,000 ft and reach FL140 by a point in space will you still be on 1013.2 when you pass FL140?