Handle ergonomics aside, because scissors aren't required to have ergonomic handles, you really want the nearer blade on the bottom so you can see exactly where the cut will be. A nearer top blade would overhang and obstruct the view of the cut line.

People talking about causing the paper to fold are really describing how they have subconsciously tilted the scissors to be able to see where they are cutting which means that the scissors are no longer slicing perpendicular to the paper.