If you use a large brush you can fill manually the full model quickly.
The fill option works in layers but only will fill areas that has been previously painted, acting like a mask. For example if you have letters in a layer and you have not painted the background using fill will allow you to change the color of the letters without modify the shape. Also Alt allows you to delete the polypaint of that layer as you would do erasing in Photoshop in a layer.
This doesn’t apply in materials as it is not possible to edit or paint materials in layers at all. Only shape, polypaint and mask are stored in layers. Once that you have layers the only way to change the material is to hide all layers, fill with material, and activate the layers again. You can paint different materials in the same object too. If done when layers are recording it won’t fill or paint with material. If you do it with layers visible but not recording it will fill the material but will revert to the original as soon you switch to another layer.
If you want to fill the color base of the object even with layers follow the same process: hide all layers to fill the base. But will fill the base color, not the layers. Any color in the layers will overlap this base.