“Only after I learned that the GPU inside the Gamecube was named Flipper did I finally understand why the developers of the emulator had gone with the name Dolphin.”
Your cause-and-effect is backwards there. The GameCube’s development code name was “Dolphin”, which in turn probably influenced the naming of the “Flipper” GPU, not the other way around. (It’s also why the product numbers start with “DOL-”, as in DOL-003 for the controller. Ditto the Wii, which was code named “Revolution” and whose products start with “RVL-”.) Dolphin the emulator took its name directly from the GameCube’s “Dolphin” code name.