In response to the original question: The ROC since the Revolution , and especially its Bolshevik/communist incarnation, was somewhere betwen outright hostile to to generally skeptical about institutional state (communist) authority, and for good reason. The Communists were militantly atheistic and would have destroyed the Church if it could have. It almost did. The Soviets undermined , weakened, and/ or coopted the ROC.
The ROC naturally distrusted the Soviet government , even in minor matters. The Ekaterinburg remains were under Soviet "control' ,so to speak, for 73 years, and the fall of Communism in Russia couldn't mitigate the ROC's distrust overnight. Having a former KGB head (Putin) as President or Prime Minister could hardly be reassuring. In a matter as sensitive to the ROC"s heart as the authentication and burial of the IF 's remains, the ROC's suspicions are almost understandable, though in this case, as the world scientific community has proved ,still excessive.
In my view, this whole thing is another unfortunate legacy of the USSR, even though it's been gone for twenty years. I hope the ROC can come around to accepting the remains as authentic without feleing it's comromising its religious tenets.