The mass must always be considered. The 2009 IBC section 1509.2 defines when a penthouse may be considered part of the story below rather than a separate story (max height, no more than 1/3 the area of the supporting roof, restrictions on type of use, etcetera). I would use that as a guide and a minimum standard and then apply some engineering judgment.
For instance: If the penthouse is a small structure with a separate lateral system and it meets the IBC requirements, I probably would not consider it to be an additional story. If the penthouse is approaching the 1/3 area limit and its lateral system is a continuation of main buildings lateral system, I might consider it to be an additional story.
This really is not an ETABS specific question. The "Structural Engineering Other Technical Topics" forum has more traffic and the question would probably get more attention in that forum.