If using a cutting disc directly in a drill that is of a larger diameter than the disc, the cut will be at a slight angle to the vertical. This can be avoided by using a narrow-handled flexi-drive, of course. However, if you end up with two cuts at a join that are angled away from each other, then there will be a permanent open gap at the top of the join, giving a 'click' that may not be the end of the world, of course.
If you are using the disc in a drill directly, then having the drill over the track that will be used, rather than the piece that is being removed, will result in joins that are closed at the top.
One extra benefit of using a cutting disc is that you are much less likely to bend the rail and cutting can also be done in much more constricted spaces than with a saw.