Sure, it could do. But for the author, (a) XML comments are simper: No need to separate the two; no need to manage crossreferencs (I've used Leanpub footnotes and know that they can easily become out of sync); (b) They are quicker to write; (c) the comments can go exactly where you need them when you are writing; (d) someone who is reading the text source can see the comments inline exactly where they are, no need to scroll etc.; (e) a good XML authoring tool would allow users to hide XML comments (similar to being able to fold programming language comments in an IDE). I've requested (e) of BareBones Software's BBEdit. ; (f) XML comments as far as I know are more general, they work in Markdown and are not restricted to particular flavours of markdown.
Background: This doesn't really matter but FYI I am asking this because I am writing a scholarly journal article in markdown. My cooauthors don't know markdown at all. I've gotten one of them a copy of Marked 2. I'd like her to be able to read the source directly in a text editor, and also read it in Marked 2.
Incidentally, no journal to my knowledge supports Markdown. I will need to go through the pain of converting the markdown to RTF. But I'd rather do that than use a word processor. There might be business opportunities for tool developers that would facilitate this task. (I haven't thought this through. I've written books in Markdown, but never journal articles before.) I'm sure there are tens of thousands of academics that would like to do what I'm doing, if they knew about Markdown and had the right tools. The unpleasant part for me will be dealing with conversion to and from Word, which is currently a 1 way process as far as I know.