The base layer is a paint layer that you can’t paint on. Its a copy of the terrain textures before any of your custom layers are applied on top. If you don’t intent on using procedural painting before applying your own custom layers on top, you don’t really need to worry about the base layer.
If you do apply procedural painting on your terrain, make sure to ‘update’ your base layer to ensure that the changes are saved. IMPORTANT: Always hide all of your custom paint layers before updating the base layer. When you hit ‘update’ on the base layer, it copies all the textures that are currently visible/painted on the actual terrain, so if your custom paint layers are visible, those will get baked into the base layer (which is not what you want)