Although it may at first seem counter-intuitive, many new motorcycles, especially those with fat rear tires, are designed with the rear tire center-line being offset from the front tire center-line.
When upright and rolling straight ahead, the center-line of the rear tire does not exactly match the center-line of the front tire.
The tire center-lines are parallel, but don't overlap.
Correct
tire alignment requires both tire center-lines being parallel when the bike is rolling upright and straight forward. The wheels are in parallel planes. But not necessarily in the same parallel plane.
Correct
sprocket alignment requires both sprockets being in the same parallel plane (regardless of the bike's position).
Being in the same parallel plane assures that the chain has a straight pull between the sprockets, irrespective of the bike's orientation.
Forcing the rear wheel into the same parallel plane as the front wheel in order to achieve matching tire center-lines may create mis-aligned sprockets.
See following links for more info:
www.motorcyclemetal.com/downloads/Harley...%20Made%20Simple.pdf
xlforum.net/vbportal/forums/archive/index.php/t-1600964.html
Good Fortune!