I am assuming that you are looking at the example profile which comes standard with BeerSmith. The reason is that someone wrote it that way to match how they operate their process and equipment.
Each of the profiles in BeerSmith is there to give people a template for customizing their own profiles to match their process and equipment. They are not a recommendation or best practice. I went to look up the stock profile for step mashing and I have long ago removed it in place of my own mash profile which reflects how I do a step mash process, so cannot give you a description of how/why the stock profile was constructed.