Hey @Naatan,
we are using the custom highlightBlock feature to only have highlistjs render the code-parts of the markdown (see https://github.com/discourse/discourse/blob/master/app/assets/javascripts/discourse/lib/syntax_highlighting.js#L21 ). Now from what I can read in the highlight.js’s source code, it internally does use the Auto-Mode if no language is specified. See line 512 in the highlightBlock function.
Can you show us an example of where and when it doesn’t work but it does with the library outside of discourse? Then I’d gladly debug it, otherwise I’d say the request needs to go to highlightjs …