I think namespaces are still a thing when it comes to extensibility (see topic Namespacing with CURIEs for my thoughts on extensions).
But core CommonMark doesn’t have namespaces yet, so limiting this topic to the spec it seems to me that <tag:foo> and <foo:tag> should be treated consistently, but as the spec is currently written, they come out quite differently as <a href="tag:foo">tag:foo</a> and <foo:tag> respectively.
I would hope this inconsistency should be resolved as soon as possible, before extensions are standardized. I think that limiting auto-link to absolute URIs (with the colon), rather than embedding a list of supported schemes would be the preferable choice to achieve such consistency. I’ll put together a pull-request with formal changes, referencing this topic for further discussion.