When you visited the license chooser in 2003, you answered three questions and were presented with some HTML you could paste into your web page. That HTML contained a comment in it, containing the machine readable license RDF/XML.
There were a few reasons for the comment approach. My recollection is that at the time there wasn't really a way to reliably embed structured data in HTML. This was before Microformats, Microdata, RDFa, etc. People occasionally suggested using a META tag, but there were issues with that, as well. (Namely, if you were using a hosted authoring system like Movable Type or Blogger, you usually didn't have control of the head of your document.)
The <!-- comment --> was the recommendation because it worked. It embedded some information, and most tools passed it through unmolested.