HyperSizer does not do anything to account for the actual taper of the stringers. It assumes for each component that the stringer spacing is constant throughout.
We are working on a capability that will allow you to dictate a number of stringers rather than a stringer spacing. This way if you have a tapered region and you split it into a number of components, then as you go from component to component, the spacing will be reduced according to the taper. However, even in this case, the stringer spacing will be assumed to be constant within each component. I would look at the stringer spacing in HyperSizer as the average stringer spacing throughout the component.