New super rugby log discussion

The new Super rugby log gives each team who are at the top of their respective conference logs to be in the top 3 on the combined log, even though teams may have more points than them. This disadvantages especially the South African and New Zealand teams as their derbys are more physical than those of the Australian teams. This year the brumbies are a full 5 points behind the teams below them but yet stay on third, is that fair on those teams who have more points?