The MAJOR problem with the "mis handling" theory is simply this. IF there was some purported "contamination" HOW was it contaminated with mtDNA that EXACTLY matched the Victoria's daughters line AND with DNA containing a VERY rare heteroplasmy exactly found in both the Nicholas II remains AND his brother George?
Actually that is relatively simple given sufficient resources and expertise.
It merely requires material from an appropriate source.
In addition, it is not true to state that the science of forensic genetics is identical nowadays to that carried out at the time of the testing. It is now well known that original statistical rarity for instance was exaggerated - ie geneticists were subsequently surprised by later developments with more accurate methods and more database of findings to discover that matching of profiles within the sequences used for testing was not anywhere near as rare as had been supposed. It is also notable that in reports of a number of recent forensic cases - for instance the disappearance of Madeline McCann - evidence was cited by the forensic investigator as being unreliable due to potential contamination. It is not difficult to achieve if the motive is sufficient. Especially in a case such as this.
Doubt has also been cast on the accuracy of the early testing by a more recent team of Japanese researchers.