Docker is in very active development and issues like this get resolved every week. That said, it's not a problem because of the service discovery and routing that would be involved in the Flynn system.
Docker 1.0 will include an API which will make it much easier to customize how you want networking to happen. That includes static IPs and private networks.
Note that the 1.0 API will also include hooks for service discovery - specifically to facilitate the development of projects like Flynn.