Do the conclusions change if we assume that the goal is not to optimize for value to the user, but for value to the company? Specifically, it seems that using the vote difference rather than the vote ratio would help controversial stories rank high. Controversial stories in turn are great at driving lots of discussion, which means lots of visits and revisits to the comment section.
(Compare to the apparent HN policy of discouraging controversy, both by the large effect of flagging and through the flamewar detector).