What matters in the calculation is the initial and final positions. If the masses move about while they are being put into place, this does not matter. It makes no difference whether $m$ moves towards $M$, or the other way round, or both move toward each other. The PE only depends on their initial and final separations.
Also, because gravity and electrostatic forces are conservative, it does not matter in what order you put the masses into position, or what route you take to get them there. You can choose whatever order and route are easiest for your calculation.