Trevor,
I disagree because a fire formed case is already tight in your chamber. We aren't talking about a two point alignment here, it's aligned along the full body of the case. For the neck to have any influence in alignment, the case body would have to be loose enough in the chamber to allow for some movement and you would have to have a second alignment point at the back of the case that is also snug and concentric to the bore. That would have to be the bolt face which is neither snug or concentric to the bore. The bolt face may be perfectly perpendicular to the axis of the bore (trued), but that is not the same as concentric.
I've also done the experiment with a slight twist: I sized the entire neck down to a diameter just above where the donut would contact the bullet with a larger bushing, and then partially with a smaller bushing to only give neck tension to the top 3/4 of the neck. It improved results with both FL and neck-only sized cases. In both cases, no portion of the neck was contacting the chamber. Further, in the absense of donuts, I don't see any improvement in groups between FL and neck-only sized brass in my tight Palma chamber, which also makes me doubt the improvment is due to alignment.