If metadata blocks (beyond the document header) are going to become a CommonMark extension, using these blocks for comments is sensible, especially as it eliminates the need for a specific Markdown comment syntax.
The Pandoc README states that a YAML metadata block can be terminated with either three hyphens or three dots. What was the reasoning behind this? I personally like the use of hyphens as a delimiter for both the start and end of the block (consistent with other parts of Markdown that use matching delimiter pairs). I see a potential clash with the horizontal rule syntax though.
By the way, syntax for meta data has been discussed extensively in the Metadata in documents and Document titles topics.