It's not only that, actually if you have sanded fine enough that is not the problem. The problem is the way metallics lay a cured finish compared to the way they lay on a fresh coat of base. You can see this by looking at your first coat of base, it will usually not look quite right until you get another coat on it because the second coat lays better on top of the first. I think it has something to do with the way the underlying coat temporarily absorbs a bit of the solvent from the fresh coat. Intercoat or clear base gives you that first coat, so the blend will lay out nicely.
But you don't need the intercoat on areas that will receive full basecoat coverage, only where the color is to be faded out on adjacent panels.