(This is too long for a comment.) According to Markdown change: Intra-word emphasis now works this is the expected behaviour. See the details section of this post. For convenience here is the actual restriction that causes this to not work:
- If a single or double asterisk is supposed to be interpreted as intra-word emphasis, it cannot have punctuation on one side; it actually must be inside a word.
I was unable to find anything newer regarding this behaviour, so I'd assume this is still in place.
There is a declined feature request for the trick that works in the normal questions: Allow HTML tags in comments.
As far as I see, there is no real workaround to that, and it is very, very unlikely that there will be a fix/enhancement for that. Comments are not meant to last. They should be used to clarify and critique; in those cases their meaning and content shall be incorporated to the post, where the full set of markdown is available.
I believe that it is reasonable to assume, that without the correct typeset, the interpretation of those names is still likely to be correct. (Apart from the cases where people do not, and never will, care about the correct typeset; but then it really does not matter.) For example, I think that "(2R)-butan-2-ol" will be understood almost as well as "(2R)-butan-2-ol".
If you feel strongly about that, you can still file a feature request (or you could transform this question into one).