What you're saying is fair enough, Cyborg, but what I was finding a bit confusing is that the high spots are clearly adjacent to ALL of the head fastening points that are visible in this photo, not just the fastenings with studs..
Which tells me that the head was over grossly over torqued at some point. To me... it illustrates the need to not only stick to the recommend torque using a decent torque wrench that was stored properly and calibrated within recent history, but to use torque plates when boring/honing cylinders. If you haven’t..... have a look at MM’s Clipper thread. Completely different setup, but it gives you an idea how how much distortion can occur. A lot! And he wasn’t over torquing things. As I mentioned before, that photo (showing the blow by at the top) goes a long way to explaining what went on here. Not the whole story, but the majority of it.
So basically what I’m saying is regardless of how the studs were installed you’d still see evidence of distortion there (around bolts and studs) just from being over torqued or bored without torque pates (plural).