Common practice for references to articles with different spellings of author's names
I suspect there is no single practice, for the simple reason that our society is very bad at dealing with the massive degree of variation found in names. 

As a matter of principle, however, I would tend to approach transliterated names in the same way that one approaches name differences within a single language (e.g., complete formal name on a dissertation vs. "preferred name" on articles; post-marriage vs. pre-marriage name; name change following change in gender identity).  Here, I see two general use cases, which fortunately correspond with the two options you identified, and it's just a matter of selecting which is most important for a particular usage.


Name as an identifier for a person: This is the use for references, either in the citations/bibliography or in prose (e.g., "As Chebyshev writes in [5]...").  In this case, you should use the same single name for the person, ignoring different historical versions, because the most important thing to communicate is the shared identity.  Since people generally are allowed to choose their own names, you should typically choose the most current accepted name, as the best reflection of the person's current identity (though there are some exceptions).
Name as a historical record: In this case, the thing to be identified is  the artifact, not the person, and any issues in the rendering of the person's name are secondary (e.g., "Festschrift for Tschebyscheff" would not be modified).


Something that I see as a somewhat problematic boundary case is when there is an "live" artifact named after a person, e.g., Chebyshev's inequality.  Here, I would recommend simply going with a recognizable version of current consensus in the community where the publication is being sent.