The ones I removed where the longer shoulder so must have been replaced at some point, as with the ARP that I installed. They both worked with the RCV and factory flanges.If your studs were the original version, yours would not be proud - and would be ok. As the lower photo in NeverFinis's #31 post shows, the studs now supplied by Toyota for the rear have been changed to the studs used in the front, which are longer. He did not mention when that change occurred.
All the studs I have on hand have the same shoulder length(longer) as shown in your drawing earlier, this is where the confusion is. Why do studs with the same shoulder length sit in drastically different depths?
You said that you where installing them finger tight, what happens if you double nut them, blue loctite and torque them in?
If it was me, I would machine a light press fit C/B into the hub, but I have a machine shop at my disposal. Non machine shop Matt would torque the stud in and stack some washers and run it without second thought.
