As far as I can tell, changes in mod status -- becoming a mod, or ceasing to be -- does not immediately affect which rooms that user owns.
When a site enters beta and gets a chatroom, the pro-tem mods are installed as owners of the site room, and the mod-only room of that site.
However, later changes in the mod team are not reflected in the list of owners, meaning that ex-mods retain access (unless any of the other owners/mods remember to take action), and new mods may not have full control (I'm not sure if they are chat-almighty by being mods, anyway).
I think that room ownership of site rooms should be synced with the moderator list automatically.