To perfectly align the disk brake, file the dropout deeper, so that the center of the motor axle is exactly on the same spot the center of the previous wheel was.
But bear in mind,, this is a permanent change, if you go back, the disc may drag on the caliper housing.
Ok to leave it alone, but some of the disc pad will be above the disc rotor. As the pads wear, it can result in the unworn part touching with no grab on the disc itself.