You can install conical washers on every bolt and stud if you like. The only small problem is that the conical washers are not always available or you might only have 6 or 7 of them. From everything I've read the conical washers "spread" the load over a larger area reducing the chances of "breaking off" a manifold ear. A bolt without a conical washer puts all the torque and pressure just under the head of the bolt in the center of the cast iron hole as opposed to around the hole in a circle away from the hole. I also think that the conical washer allows the manifold to expand/contract (heat expansion/cooling) because these special washers only make contact on their perimeter. If you examine a conical washer real close you'll see that they only make contact in a very small area (along the outer edge). The manifold holes that are thick should also have flat washer (hardened) so that the bolt doesn't dig into the manifold which would keep it from expanding and contracting. But Mopar does use the conical washers on all the bolts/studs as far as I know, even on the more modern Jeep engines.
Some of this is theory, I'm sure the Mopar engineers had a good reason for using the conical washer.
I keep the conical washers in stock in case anyone who buys my manifolds needs any. Since they don't add any weight to the shipping box the shipping on the washers is almost nothing.