The packaging machines and the employees running them would have had to know
which minifigure would go into each box and sealed carton, so there has to be
some kind of method of identifying them.
Each figure would be packaged by separate machines and those packaged figures
would be brought separately to the machine that packs them in the case. So to
the extent that the packing machine "identifies" them, it would do so
by the place they were coming in.
I don't buy that theory at all. It's not how TLG operates their production
lines.
It's a known fact that TLG use a production code system that ensures that
they can trace all of their production. What makes you think they'd stop
doing that?
Their warehousing system has to know where everything is stored, anyway. So there's
an identification system they're using that is so good that they can even
send out employees to fix production errors that made it out to sets in stores.