The problem is that unless two properties are actually going to work the same way, we can't use the same prefix. We have to be able to target individual, misbehaving browsers.
Its not just IE that's quirky - Firefox, Chrome, and Safari all have CSS bugs that have to be accounted for. Its hard enough to target them individually now, but under your proposal it would be nearly impossible.
But of course, this is not what the author is discussing at all. He doesn't have a problem with vendor specific prefixes in general, but rather feels they should be deprecated more aggressively once widespread adoption occurs.