I think WordPress needs dedicated filters to be applied on content and excerpt immediately when they are retrieved from the database, to be used by formatting filters such as Markdown.
I like Markdown, but I was having problems with how WordPress does not pass the complete article to it when the “more tag” is used, and when forming RSS descriptions. Markdown uses shorthand link tags that would normally be resolved with references placed at the end of the document. With the truncation, links were not being resolved, and what’s worse, Markdown notation was left in the resulting display.
I created a patch that fixes the problem for my current articles. However, I think multipage entries would still have this problem, so this patch is not sufficient. Also, I’m not sure if I’m causing undesirable side-effects by moving the the_excerpt filter further up in the code.
Before I start working on the filters to be applied on database retrieval, I’m waiting to hear back from WordPress developers about the approach, to avoid wasted work.