Dear Bob and all,
I can answer the question about the church recognition as it was explained to me.
The reason that the Patriarchal branch of the Orthodox Church (as opposed to the Synodal Branch in exile) refused to recognize the bones has nothing to do with whether or not they doubted the veracity of the DNA evidence.
The Romanovs were declared saints by the Church in Exile in the 1980s, and only by the Moscow Patriarchate in 2000.
The two churches have been in a tense and difficult negotiation since the fall of communism about reunification. Much of the acrimony has to do with real estate in the Holy Land and around the world.
One of the requirements of the Church in exile was that Moscow recognize the 1980's canonization of the Imperial Family. Moscow did so in 2000.
This is the problem -- the ritual for burial of saints is one religious service, while the interrment of an imperial family member is another. The bones and relics of saints are supposed to be venerated in churches, not to be buried.
By "not recognizing" the bones, the Moscow church was able to allow the interrment in the Sts. Peter and Paul Fortress without having to open the sainthood issue with the Russian government.
Now that the martyrs are buried, and the Church has recognized them, they are already interred, and the Patriarchate doesn't need to worry about dividing and distributing the bones as relics.
Once the church in Ekaterinburg is finished I bet there will be discussion about moving some or all of the bones to the site of their martyrdom.
Nick