Theory: Gloomy Galleon is the Sunken Crocodile Isle

Abstract
Gloomy Galleon from Donkey Kong 64 represents the remnants of Crocodile Isle, after it sunk in Donkey Kong Country 2: Diddy's Kong Quest / Donkey Kong Land 2.

Arguments

 * Argument 1: Clapper was first introduced on Crocodile Isle in Donkey Kong Country 2. A Seal resembling the appearance of Clapper appears in Gloomy Galleon during Donkey Kong 64.


 * Argument 2: Gloomy Galleon is accessed through a portal on the K. Rool's mechanical Crocodile Isle, a mobile fortress that couldn't possibly house a deep cliffside cove. However, the portal being placed on K. Rool’s mechanical Island connects it to the Kremlings.


 * Argument 3: In the Donkey Kong 64 manual, the area is referred to as "reptilian lagoons”, clearly connecting it to the Kremlings.


 * Argument 4: The Gangplank Galleon's last appearance was in Donkey Kong Country 2: Diddy's Kong Quest, where it was beached on Crocodile Isle, before it was seen sinking with the rest of Crocodile Isle. The ship was likely destroyed or highly damaged during the destruction of Crocodile Isle. The shipwrecks found in Gloomy Galleon are referred to as the "the gloomy, rotting remains of the King’s once proud armada" in the Donkey Kong 64 Manual. This could suggest that the Shipwrecks were part of the Gangplank Galleon or some of the other stranded ships on Crocodile Isle, such as the ones found in Crocodile Cauldron and Krem Quay.