In my opinion, that doesn't really affect much. Very few people are going to get below 60/100 after alignment. I would say that over 99% of the people considering applying for commerce will get it. I believe that they only implemented this to artificially raise their UAI cutoffs, as many students associate UAI cutoffs to quality of the course.
So say if this bonus points thing isn't implemented, the UAI cutoff might be 85 for commerce. With this bonus points scheme, they can report that their UAI cutoff was 91. Then the next year, students look at the UAI cutoffs, and they see a UAI cutoff of 91, then they go "hmm... such a high cutoff, it must be a good course...". Therefore, although on the surface it may seem that they are promoting commerce courses to less intelligent students, they are actually the opposite and are attracting future students with high UAIs to consider ANU.
So basically, it should not affect your chances of getting into the course, as almost everybody applying will get those bonus points.