If the rotor is hub-centric on the axle rotor register, than it doesn't matter how big you oversize the wheel stud holes in the rotor...just make them large enough to clear the shoulders on the wheel studs and call it a day.
If the rotor is not hub-centric, then size the wheel stud clearance holes in the rotor for the shoulder diameter of the wheel studs, and let them locate the rotor.
If you need to machine down the axle flange diameter for the rotor to properly seat fully, then reduce that diameter accordingly and/or add a chamfer to achieve the desired result. As long as you have at least 1/8" of material outside of the wheel stud knurl diameter, you should be fine.
In a properly setup rear disc brake kit, the wheel studs should be in pure tension and won't see any shear loads due to the brake forces, as the rotor is sandwiched between the wheel and axle such that the only way that could happen would be if you didn't adequately tighten/torque the lug nuts.
Tobin