We're not talking about HTML, we're talking about PDF, where everything is supposed to come from one source (99.99999% of the time; Adobe introduced this Javascript embedding nonsense, but you shouldn't ever enable it).
As far as HTML goes, sandboxing the HTML rendering thread is an important step towards shutting down browser-based attacks. At the end of the day, perfect security is impossible-- yes, even in Java. However, additional layers of security can add to your confidence level. BTW, if you haven't read "reflections on trusting trust," you should check that out.