Quite honestly, there's no discernible difference whether a PDF is hosted on S3 or in Marketo itself. You could make a slight argument for using S3 if only for Cloudfront. When it comes to tracking any PDF, you do generally need to have JS fire to record that the PDF was viewed before the PDF itself is served to the user; typically that's either done with an intermediate page or a slight delay on the previous page for any Google Analytics/Marketo Munchkin/etc. trackers to fire.
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I agree with Courtney, the only advantage is that you can find it in one place (Marketo) instead of looking around