Rubber roofs are a MF'er to put out, it gets under there and just burns likes crazy. Only way to get to it is start cutting off the rubber and get ahead of it and get under it. That thick heavy black smoke is all from the rubber, prob not a lot of fire just a lot of burning rubber.
Either way it's a ton of work, we've done a lot of training of these types of roofs and they're always a pain.