Maybe they laser-trim the embedded crystal in situ after the chip has been fully packaged? It might be more difficult to keep it in spec if they trim it earlier and then pass it through more manufacturing steps afterwards.

Seems unlikely it would fall out of spec by that much just during manufacturing. These things drift due to temperature (or even vibrations) anyway, and when it comes to using them in an RTC you have drift adjustment registers for any major drift from the factory.