Google Scholar: Will having HTML and PDF in different subdirectories lead to incorrect indexing?
Google Scholar is pretty smart about these things.  On all of the websites I'm involved with, we keep the PDFs in a separate directory from the page that links to them, and Scholar finds them just fine.  Of course, we also don't us the citation_pdf_url tag, so maybe we're fine because we're low-tech and Scholar does the inference for us...

I recommend doing it the easy way, and trusting Scholar to be smart.  If it doesn't do the right thing, then you can always go back and drop the tag and wait for a refresh.  And then if that doesn't work, you can do it the hard way.