Presumably there would be more opportunities for secure handshaking with a proprietary port. It doesn't need to involve security by obscurity -- it just needs not to be barkingly stupid.

The best practices in auto security are probably reflected by whatever the leading Japanese brands are doing these days. Traditionally Hondas have been the biggest theft targets, but a glance at the list of most-stolen cars in America ( http://editorial.autos.msn.com/article.aspx?cp-documentid=43... ) suggests that they've more or less solved the problem, as of the mid-1990s. I seriously doubt there's that much need for further innovation.