My thought is quite close to you but explain in different way. Not relate to the bolt, then you may add this at bullet 3.
Since my past experience ever found one new rotor that cause high vibration but it was due to the high excentricity from the factory. Then from deep investigation then found that each of disk, when check to the cross section there are not 100% perpendicular nor the disk thickness at each side could not make a 3 wheels (when we tight the tie bolts on) to be bundle and made a straight rotor. Then after check to the thickness in micro meter to each face of disk then decision to do realign the disk face (by rotate disk and make each face to offset each other and could made a new rotor bundle as straight rotor as much as possible). Then later on we can make a new rotor assemble to be straight and could got to be lowest vibration. My point is normally at the factory, they normally do this task as well. Due to each faces of disk must be check and target to assemble them to get the straight rotor.