Sorry, I'm not sure what you mean. You can set both the diffuseMap and diffuse properties of a material. And if a diffuseMap is set, diffuse is only taken into account if tint is enabled.
Sure, just query the material you want. For example, in the Chrome console, to set the material of the first mesh instance of the model of an entity called 'Some Entity', you'd do:
someEntity = pc.app.root.findByName('Some Entity');
material = someEntity.model.meshInstances.material;
material.diffuse.set(1, 0, 0);