What changes in a PDF workflow is productivity. Coming from a Brisque standpoint (ROOM workflow) and migrating to a Prinergy PDF workflow, I can attest to that. Granted that 2% error ratio is rare, but the overall productivity makes up for that, easily.
One of the errors I can think of ATM is type not getting rendered on plates at 2400dpi. The low res 300 dpi virtual proof shows otherwise. However, it's very rare (and might have something to do with obscure fonts) but that issue has been forwarded to Adobe last year and may have already been resolved.