> it's about how to tell the source highlighter to ignore specific lines (e.g. consider them comment lines) so that Asciidoctor can take over and format the line as a link.

What you're probably looking for is a custom syntax highlighter adapter, which is also an extension point. It is invoked by the converter when it needs to apply syntax highlighting to a source block. This seems to be the perfect opportunity to do the processing you want to do.

Here's an example: https://github.com/asciidoctor/asciidoctor/blob/master/lib/asciidoctor/syntax_highlighter/rouge.rb

If you want to reuse a built-in adapter, you can extend it by looking it up, and extending the resolved class.

-Dan