I love your take that Zeus is a system thanks to him eating Metis! How does that work? Does Athena know?
Actually, Athena used to be part of the system as well! As gods, they have much more leeway. So she separated from the system and became a physical form. It's why she came from his head, and why she was fully grown and donned armor.
She and Metis were close, like mother and daughter, and eventually more like sisters. She knows Metis well and so it may seem like she can still "hear" Metis while talking to Zeus. This can lead to her saying things like "You know she's so upset with you for that," or "She wants [x] and you're not paying attention."
She doesn't exactly see Zeus as a "dad," but understands that he sees her as a daughter. She understands that everyone else sees it a certain way, and she's come to accept it.