When you advocate an add-on to an existing solution, you're changing the solution. It's like people who recommend typescript in reply to JS's lack of types, or Coffeescript to its ugly syntax: you can't have both, they change the original thing. Or vimperator with firefox, or vim-mode emacs, or... it's all not the same thing anymore. You push the carpet down in one place, it comes up in another.
CSS still requires the vendor prefixes. If autoprefixer is the perfect solution to that, let's stop people everywhere from using vanilla CSS and switch them over to "CSS + autoprefixer". Turns out it's not that easy, which gives the original "but it requires prefixes" argument more meat.