Well, the problem with thinking that they were correctly counting the bodies is that.... two bodies are missing!
Seriously, I can see the value in counting the bodies -- but at some point that night, the Bolsheviks lost two of them. After that time, any claims of correct counts of eleven have to be lies. The difficulty is in determining when the bodies went missing -- if we could do that, then we'd have a better idea of who was lying.
I'm comfortable with the idea that they were discovered missing fairly early in the course of the night. I can't remember which it was off the top of my head, but it was either Princess Helen or her secretary Smirnov who recounted the armed house to house searches for missing Romanovs early on the morning of 17 July, at either 6 or 7 o'clock. And there were searches conducted by armed and mounted groups of men along the Koptiyaki Road all that day. So these bodies went missing early -- in the first couple of hours after the murders. And the fact that searches were made both in town and out in the woods makes it evident that the Bolsheviks didn't know exactly when they lost them either.
So if the bodies went missing from the courtyard of the Ipatiev House, then no correct count of eleven could ever have been made, making everyone a covering-up liar. But if they disappeared from the truck in the forest, the first count made by Kudrin and a probable second count made at the time the bodies were re-loaded onto the truck after pushing the truck from the grade crossing on which it had become stuck were probably right.
In the final analysis though, it hardly matters. The Bolsheviks lost two Romanovs that night, and any idea of what happened to them can only be a theory.