Having a robust comment system would be nice (especially if doing any collaborative work).
In the mean time you could look at these two options:
Inline Comment structure:
You can use comment structure similar to html comment format to make inline comments. Anything in the comment isn’t rendered. They do count toward wordcount however.
Bob walked quickly <!-- find a better verb for this --> to the window
Will show this in preview:
Bob walked quickly to the window
You can use standard footnote syntax to make footnotes in your text. They also count toward word count.