One thing I'd like to be able to do is define templates that then determine how highlight exports are formatted. Since I use Command mainly as an annotation layer for the web and then as a tool for the ingestion of these annotations into my note taking app, this would save me much work then reformatting the exports to fit my needs.

As with many of my requests, see Worldbrain's Memex for an example implementation:

Their implementation has weaknesses though, so should you get around to implementing this I will gladly spent some time extending this request.