Yes, the longer shoulder on the studs is what centers the rotor on the hub. I don't recall the part number studs I used, but those look like them. The lug holes in the rotors are quite large. I want to say they are around 5/8". This is another reason I wanted the shoulder because the rotor would have been able to move on the threaded portion of the 1/2" stud. The .0275" difference in the bolt pattern is easily overcome by large holes in the rotor. What I should have done is had the center of the hub turned down to match the center hole of the rotor. I don't recall the size difference but it wasn't much. I just opened it up with a die grinder and sent it. I didn't put a dial indicator on the outside of the rotor, but I did spin in it while closely watching the clearance to the caliper. My eyeball measurement showed zero runout and I have no vibration.
I think you may be overthinking it (not a bad thing). If I were to do it again, I'd turn the OD of the hub down a touch so the rotor fit perfectly. Other than that, it's quite easy. If I remember correctly, the Mustang rotor center hole was a bit smaller also.
I did consider drilling and tapping the rotor/hub to hold the rotor on, but it didn't seem necessary after everything was fit up. The brake pads pretty much hold the rotor in place when the wheel is off.