Welcome to healthcare Magic!
One thing is for sure that the indentation at the back of the head are a chance finding because irregular surface of the occipital bone
is the rule because it has rough surface to give attachment to the strong muscles of the head and neck. They are not important cause of headache even if they are prominent or have become prominent.
Your headache might be related to cluster headache
or a variant of migraine
or a tension headache
You need a thorough evaluation by an experienced physician and manage the headache accordingly.
Wish you a great health!