Well, that link you posted does specifically say, "New Beetle, integration with factory HU, no cutting of harness", so I'd guess it'd work as long as you're still using the factory HU.
I've been looking at this kind of thing to add to my Golf too. I'm happy enough with the stock speakers to not replace them all, but a sub would be nice. Shame I don't have the cash spare.

Does the NB still have the Premium VI single DIN head unit? If it does then the easiest way to integrate the empeg is to use an adapter from www.rcainput.com . The adapter mimics the CD changer as far as the HU is concerned. Works very well, although it could use better grounding.