I think the biggest problem with the remains is that after such a long time of lies and deception, false explanations and scams, nobody truely believed the russian authorities any more.
Had the csar and his family really died in the cellar? Most likely yes, however even here is no foolproof evidence.
Apparently the execution had been a hellish superkill. With people riddled with bullets, that still failed to cause instant death.
There have been numerous reports that the girls wore "bullet proof vests", the women had sewn their jewels into the bodice of their clothes, hoping they could hide them that way and eventually carry them into freedom. Those diamonds and stones however worked as repellents and proof vests, richocheting the bullets thus causing the girls to sustain shotwounds mainly to the arms, legs and lower abdomen, inflicting tremendous amount of pain without killing instantly. Reports say that after the rifles had been shot empty, some of the girls were still alive and then stabbed to death. Apparently when the bodies were moved, the soldiers noticed that still not all were dead and again the stabbing started. By now however the mood had changed tremendously. Where before the men had been in a hysterical state of fanatical haze and hatred, eager to kill, they were now slowly waking up out of this red haze and to their horror saw the incredible agony and terror they had inflicted on the young girls. This mood shift IMo is responsible for most of the blurred reports of burning the corpses, burying, detonating little bombs in the mine, reports of some girls (boy) escaping. None of the soldiers had a clear memory of what happened. Some clung to the official versions, even insisting that it had been them who fired the fatal shot at the csar, some on the other hand came to reject their involvement and perhaps fantasize about helping one of the victims to escape.
I however doubt that.
In any way, the remains of the csars family only reminded people, russian and internationally of the atrocities done to the innocent children. So the government decided at one point in time it would serve them better to produce the bodies, have a lavish funeral, and bury the Romanows once and for all. They are done now, it really doesn't matter if not all bones or even all bodies or the real Romanows were buried.