You may have misread my comment. If your axle is straight, and the stub axle has been made true, then it would not matter which side you tightened first when checking for warpage on each swing arm flange. If you tighten one side and it causes the other side to move away from the adjuster bolt, and vice versa, then surely it could mean those flange are warped like I found with mine. You should not have to force one side to line up if all is true. Putting the rear brake on to centralize the rear brake is a given but doing that wont counteract a bent flange.
An aside here though. How many people do the mounting nut up tight on the rear brake pivot? By doing so, it eliminates any self balancing or centralizing of thepivot between the shoes. [ just a theory I have and its the auto engineer in me asking ]