If I were to build a web app that uses markdown, I would make separate text fields for metadata anyway. I think the YAML metadata header is mainly useful if you work directly with (plain-text/markdown) files instead of web apps with potentially multiple text fields.
As such, metadata blocks should certainly be extensions and not “core spec”, because it doesn’t really make sense for client-side implementation, and as @vitaly said is hard to implement. This would save us the confusion of differentiating between a full YAML and a mini YAML, either an implementation supports it or it doesn’t, both is fine.