[Adger Smith]

I'm sure that is what you found, but you if you had moved down about 11/2 " below the studs that is where the "real difference" is seen. Studs apply more torque load to the actual structure they are installed in than bolts. The wrinkle that always comes in a bore is way different with studs. What you did was see the difference in the movement in the thread pitch area. That is the tread of the block trying to separate from the thread of the bolt or stud. Since both thread pitches are the same the only difference is the applied torque load. That can be different because of the fine thread of the stud's nut and the bolt with no nut with a fine pitch.
Look in the picture about 2 " below the deck. See where the combustion gasses have been leaking past. That is where the real leakage usually happens. There is a very slight wrinkle in the cylinder there. Its location & size in each cylinder will vary due to the wall thickness/strength of the wall. This wrinkle is also the reason that one should use the same length bolts in a stress plate as what comes through the head you are using. It is real hard to measure with a dial bore gauge because you assume that the point across the bore is straight. I had a buddy that was in Engineering school with me that went on to be a bridge structural engineer. If I want to talk about bolts and studs I had better have atleast an afternoon to spend listening to him. If you are spending the effort to do a good job I think it is best to do the bore and hone with the fasteners in the torque plate installed just like you are going to use in final assembly.