This is a good point, the list markers might not match the rendered output. I’ve been assuming that authors would update their lists to the actual letter used, e.g.
a. First item b. Second item c. Third item
instead of the lazy style:
a. First item a. Second item a. Third item
It would only be in the first case that authors could accurately refer the starting letter. However, I also think that at least in smaller documents, the author would clean up their lists to use the literal letter marker, and manually change the letter to refer to the correct list item in other parts of the text. This is, after all, what you would do in a plain text file, which is what Markdown is in it’s raw form. The advantage of doing it this way, rather than requiring a special reference syntax, is that authors can create and refer to letter ordered list without any special knowledge besides how to write a plain text document; this makes the syntax ideal for casual forum posts, etc.
Perhaps some kind of reference syntax (similar to how links and footnotes work) should be added for more complex scenarios.