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The article you cited answers your question. https://en.wikipedia.org/wiki/Craniotomy The amount of skull that needs to be removed depends on the type of surgery being performed. The bone flap is then replaced using titanium plates and screws or another form of fixation (wire, suture, etc.).

I am a layman, no expert on human skulls. I do think I can likely help you feel a little less concern perhaps. The type of xray used by orthodonists typically is called a cephalometric xray or ceph. The image I see of you seems pretty typical & many seem to show some amount of a thicker area along the occipital bun on the back of the head. Here is ...