Automatic Pro-rata was a relatively recent addition to YC.
(i.e. when we went through in 2009 it did not exist) It also clearly isn't scaleable without infinite capital.
Plus, if you had complete information, why would you ever want to automatically invest any time a company in your portfolio raised money?
My guess is the only reason they made it automatic, was to minimize the impact of a negative signal. It sounds like they hope the new changes will still minimize that signal.