Dr. Spengler just made another point in his latest review:
http://www.adventuresinpoortaste.com...part-1-review/
You don't want to have The Christmas Aliens too close to the second Usagi crossover, because the Ultimate Daimyo had been sick for a long ass time in that, but was alive and well for Christmas dinner.
He's also right that, thematically, it definitely feels like an epilogue to season 2.