Hi!
Careful, this is one of the most debated and dramatic style issues after citation format! Actual transliteration should clearly follow scientific/ISO standards https://en.wikipedia.org/wiki/Scientific_transliteration_of_Cyrillic .
Well, "scientific/ISO standards" is in this case at least three different standards, and 11 standards if you include commonly used ones :) E.g. see: https://en.wikipedia.org/wiki/Romanization_of_Russian
However the labels and aliases are in languages like "it" and "fr", so they're supposedly translations rather than mere transliterations. This makes things more complex.
Yes. I see that the bot is setting language labels for entities, so for this both language-specific transliterations and common usage can be important. Which for Russian for example can be quite crazy, https://www.wikidata.org/wiki/Q187349%27s last name is "Ватсон" but https://www.wikidata.org/wiki/Q1187613%27s is "Уотсон". And I have no idea what is the correct romanization of https://www.wikidata.org/wiki/Q4105300%27s name.