Similar situation here. Multiple dwellings were built with a roof deck, and the stairs terminated in a room on the deck with a roof. Three full stories AGP with a roof deck and stair "room". This was all prior to my arrival. They were permitted under the IRC, though not through any critical analysis, just allowed without question. So of course, folks are now wanting to add on to the little room, like a bathroom, a closet, a kitchen, etc. Just in case you might ask...I don't remember exactly what the outcome was of the one I was involved with...it was removed from my work load after I started down this path. I can see allowing them as an IRC dwelling, even with the little stair access room, but in doing so you are kicking the can down the road if it's not done through some sort of formal process to limit future additions. IMHO, these could have been permitted with an alternate request or code modification that came with stipulations.
The big difference for us is that as an IRC dwelling we have no fire suppression, but in the IBC we do.