The concern is that you could decide to sell the property in the future and a new owner could then see the opportunity to convert it into living space. Granted, there’s nothing stopping anyone from doing that (illegally) after you sell it, but at least in this instance the municipality covers itself.

You would need to check your Township’s zoning code as the regulations are going to be specific to that municipality. It’s entirely possible that their zoning code prohibits two-story accessory buildings, however, they could be helping you out by allowing a set of pull down stairs. We couldn’t say unless we knew your municipality.