Yes, flagging is implemented independent of bookmarking. We do indeed plan to integrate more deeply with the core product in this area, but that is something of a longer term project, and we felt that this use case was so important for iPad, that it was worth going ahead with it as an iPad-local feature.
As for a phone implementation, we believe that phone usage is directed and task-oriented, while the tablet sweet spot is reading and browsing. And we've designed the feature set of the two apps accordingly. So, we don't currently have plans to bring a phone-local version of flagging to the mobile interface. However, as we move toward a product-wide implementation of a flagging-like feature in the future, we'd sure like to support something like "mark this on your phone for later reading on any other Jive interface."