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I recently ran into this issue as well.

the black parts of the texture are supposed to be transparent.

I don't know how to work with textures in godot directly yet, so what i've done is open the file in blender, go into the shader editor for the textures with transparency (the node editor) and make sure the transparency node from the image (image alpha) is hooked up to the BSDF, and then make sure that under the texture properties I set the blend mode and transparency mode to alpha settings (I prefer alpha blend and alpha hashed), and then I re-exported it as a glb for godot.

just use the alpha

Replying to this incase anyone else has this issue in the future. To fix this just enable the transparency tab in the material settings.