I'm not a fastener engineer, but I'll take my best guess at it.

First of all you need to think about the total length of a rod fastener vs. a main cap fastener. If you use a bolt on the main cap, a large portion of your torque is actually twisting the bolt itself, not threading it in further. So the force is transfered through the large shaft of the bolt, before it can get to threads. Since the main bolts are very long, this creates a twisting problem (think torsion bar). If you put a stud in it, the force is immidiately put on the nut to tighten the fastener. It doesn't have to go down the shaft of the stud to get to apply the energy to tighten it.

Rod bolts are obviously much shorter, and don't have to deal with this problem. Also, if you think about putting studs in a rod, the top portion of the stud is actually fairly thin. That thin section is the only thing preventing that stud from pulling through the rod. Also, this creates a very high stress concentration at that loading point. Where as if you put a bolt in it, the threads help distribute the load through the rod more evenly.

Lastly as mentioned, the profile of the rod can be trimmed down (lighter, more clearance, etc...) if you use a bolt.

Like I said, I'm not a fastener engineer so someone may tell me I'm wrong?

But that's how I see it...