Torque is torque, does not matter the fastener. You can torque a stud to stock specs and the cap will have the same clamping force/distortion as a bolt. Even with identical torque though the stud can be tight sometimes due to the size of the hole in the main cap and cause misalignment, also the lower torque setting will negate some clamping force therefore somewhat reducing the advantage of studs. Bolts to bolts is definitely not an issue if the torque is the same. The only real way to know if things are "right" is to check clearances.
