There is if you want to give the link your own title rather than having it inferred from the target URL, i.e. [title](url). Giving the link a title wouldn’t indicate any preference for URL rewriting so I agree with @mattmccutchen that 1 and 2 should behave consistently for URL rewriting.
There could be an argument for the title exactly matching the URL being an indication that it shouldn’t be rewritten but what if a user wants to provide a title and wants the URL to not be rewritten? There needs to be some other method of specifying that.
Something that comes to mind would be a title suffix similar to embedded image sizing, though I’m not sure how a user would discover that.
An embedded image can be sized like this:
So the discourse-github plugin could (presumably) be made to look for something like this:
[title|github-no-rewrite](url)