Can routed ships retreat to port in the same sea area?
The port is never considered "part" of the sea area; control of a port depends on whoever controls the land area, and the sea area is merely adjacent.  The ability to use a port despite the adjacent sea area being occupied is probably the most important aspect of ports.

From the FAQ:


  Q: Can a fleet that is defeated in a sea area retreat to a friendly Port touching that sea area?
  
  A: Yes.