If you are removing the rotors because they are below min. thickness and need to be replaced, you can ignore the "indexing". The problem comes if the axle flange is not perpindicular to the axle centerline. If that's the case, no amont of rotor machining will correct the "runout" caused by that.
If you are removing the rotors because you believe there is runout and are going to machine the rotors in an attempt to eliminate that, you first need to determine of the problem truly is a warped rotor or if you have a problem with wheel bearing clearance.
If the problem is the rear bearing(s), that needs to be addressed, first.
The procedure is:
1) Validate bearing clearances and repair as necessary.
2) True the axle flanges.
3) Machine the rotors if necessary.
A C2/C3 disc brake will tolerate a maximum of .010 runout before the sealing system fails and the brake "sucks" air. It doesn't matter from where the runout comes...bearings, hub or axle flange or rotor...but the cumulative number needs to be .010-in. or less.