They have decided to declare that slug guns are shotguns currently if they are chambered in a shotgun caliber.
You are right in your understanding that they are technicaly rifles. They are simply a rifle operating at low pressures with a large bore.
Many of these things are decided by what policies the ATF chooses to adopt. They can change thier policies on a whim, and thier policies have the force of law without being law. A shoestring can be made a machinegun by declaration of a policy change, and then reversed later. They have numerous laws they can choose to interpret in different ways, and since they are given the authority to interpret the existing laws, they can create whatever reality they wish. A single law can be the basis of 10 official interpretations or 100 interpretations that are given the power of law.
Of course if they step too far outside reality and a court of law corrects them, a precedent is set on that subject. There is then case law on that subject and they must abide by it under 'Stare decisis' (or interprete it in ways not specificly opposed by the court once again, until those interpretations are addressed in a future case.) So they usualy stay within a version of reality that is generaly acceptable so as to not be corrected by a court and lose some power of discretion on a given issue.
Currently slug guns are considered shotguns. They will probably continue to be considered shotguns for the forseeable future. People have written them and recieved replies that yes they are shotguns. So the industry considers them shotguns.
Under the law however you are right, they could be considered rifles with bores illegaly in excess of .50 caliber.
Besides the law they are also rifles under the plain english meaning of the word. They are portable long arms with rifled bores designed to fire a single projectile that is imparted a spin by that rifling. So yes they are rifles.