Theory: Bone Goombas are wearing Goombrat skulls

Abstract
Bone Goombas are not undead Goombas, but Gloombas wearing Goombrat skulls.

Arguments

 * Argument 1: Goomba skulls, seen in Mario Party 4's "Mushroom Medic" don't resemble Bone Goomba skulls in the slightest.


 * Argument 2: In New Super Mario Bros. 2, when a Bone Goomba is defeated, their skulls come off and reveals a regular Goomba face underneath. In Paper Mario: Color Splash, Bone Goombas call their skulls "bone masks". Their skin has a very similar blue hue to the skin of Gloombas.


 * Argument 3: They don't look or behave like other undead enemies found in New Super Mario Bros. 2 (the game that they were introduced), those being Bone Piranha Plants, Fish Bones and Dry Bones. Bone Goombas clearly aren't just a skeleton and also don't have fire immunity.


 * Argument 4: Bone Goomba's "skull" highly resembles the head of a Goombrat, whose most identifiable features are the two square upper teeth and the large furrowed brow.