Just as a point of information -- do all transponders use thumbwheel switches or one-button-per-digit? While these were common in certain classes of radio equipment a few years back, as far as I'm aware most such applications now use a keypad plus some form of execute/load button.
That has the advantage that you can't select an intermediate code while you're changing the settings, but does mean that if you don't press the execute button properly you're left thinking that the code displayed has been accepted while the equipment is still using the old one. Good user interface design (UID) can minimise the chance of this happening, through a number of strategies.
I'dve thought that in any case better UID could sort out this problem, leaving the transponder active on the old setting during the process of changing the code while ensuring the code IS changed safely, even during very busy or choppy times. In this particular case, the fact that the safety aspects are so pressing and that both modes of use -- going to standby during change, or leaving it active -- have their downsides makes me think that this is a good case for getting some kind of fix into the works.
R