We save the time from Polish deck checks by not giving the three minutes to shuffle. I don't think that this means you should prevent players from shuffling. Simply explain what has happened (i.e. your decks are in the same, random order, in which you gave them to us) and why that means that there will be no additional time for shuffling.

By imposing these rules on players, we end up with situations like this, where we're trying to apply policies that as already mentioned, usually govern what's happening inside a game of Magic. Our goal is time, and we can maintain that and have players on our side by simply explaining what we're doing, rather than making it stranger and harder to accept for them.

Just my $0.02.