There are a few misconceptions here. Yes, your current altitude is sent out with reference to STD and corrected by ATC's systems for QNH. An erroneous QNH setting will have no effect on ATC's end. However the selected altitude that some ATC systems can see through the Mode S ES is referenced to the QNH set on the FCU even if the altimeter is in STD mode.
So there is no problem with going to QNH on the altimeter, preselecting your QNH, and returning to STD. The only caveat is that if the QNH setting is very different from standard and ATC happens to look at your selected altitude, then they could query you as to what altitude you are going to level off at. In which case you can just set the QNH to 1013 / 29.92 and everyone's happy.
Personally I set the QNH where the SOP says to set the QNH (just before transition level). However until this point the QNH set on the altimeter is some random setting from 7 hours ago and ATC has never complained so the preset method suggested above really isn't a problem.