A stud, being fully threaded, will be more flexible in extension than the same nominal size, partially-threaded bolt or cap screw (the unthreaded portion of a bolt has a slightly higher stress area, thus is slightly stiffer than the threaded portion). Thus, a stud may produce a slightly lower clamp load for the same extension as a bolt. For the same applied torque, there is no difference, except:
Depending on the type of cap screw and type of nut, differences in the head size (bearing area or contact area) can/may affect the relationship of torque vs. preload.
Both effects are likely pretty small (less than the error inherent in estimating preload from torque alone).