What’s the problem? That the PDF is not embedded? I think you can achieve this by putting an exclamation mark before the link. In any case, if there are issues with Yarle, just open a ticket on the Yarle issue tracker. The author is very responsive.
I have converted my Evernote database with Yarle and it worked quite well. Sure, there is always something you can improve if there is complex formatting involved. But with Yarle you can also save the original HTML from Evernote and put a link to it in the Markdown note. That way you can always view the original if Yarle broke something while converting to Markdown.