Here's a story the might shed some light on the subject. Once in the early 70's a friend's 750 Atlas developed cracks right above the cylinder flange. We took it to a very capable specialist. He put a strobe light on the motor while it was running and I was flat stunned by what I saw. I had been operating on the assumption that these motors were a rigid assembly, but boy, was I wrong. We could see the entire head and cylinder grow and shrink, once slowed down by the strobe under the influences of those barely contained explosions going on inside the motor. It basically looked like Jello wobbling around....
Adding to that, I once had a customer who complained that his head bolts wouldn't stay tight. I assumed correctly that he was tightening them too tight and had stretched the bolts beyond their elasticity.
New bolts and much less torque solved his problem.
What helps to understand this is that there is a difference in the expansion rates and amounts of steel, vs. aluminum. Aluminum heats up quicker and expands more than steel or iron. Once everything has achieved proper running temperature, the motor settles down. Before that, things are moving around quite a bit. There is much more movement between parts in this type of motor than you might expect.
And fret marks like you describe here would be a result of that movement.
It's basic physics. Scratching your head and musing on the design can help with understanding of what is actually happening inside that motor.