For Minimap buttons to be skinned the Skin Buttons option of UI Frames --> MinimapMap Buttons Options must be enabled as well as the Buttons option of Modules -- > Button Settings.
The Objective Tracker option is Player Frames --> Tracker Frame --> Skin Frame. This only skins the frame, the Header textures are removed by default. At the moment to disable skinning any of it you also need to uncheck the AutoPopUp Frames option. I can add an option to skin the Blocks if required.