How does the flexing of cranial bones relate to the glymphatic system that clears waste from the brain during sleep? It's hypothesized that the neurons use less ATP when not active during sleep, so they require less oxygen, reducing blood flow to the region, which in turn increases the flow of CSF. Maybe the rhythmic motion of the cranial bones is also involved in these waves of CSF, similar to how muscle contractions help propel lymph through the body to the collecting ducts. It's accepted that poor craniofacial development causes airway restrictions that inhibit deep, restful sleep and keep the sympathetic nervous system turned on, but maybe immobile cranial bones also play a role, preventing the neurons from shutting down and reducing glymphatic clearance. Good breathing seems to be a link between achieving restorative sleep cycles and cranial bone mobility.

There's certain muscles that pulses the cranial fluid. Also the heart is able to pump that fluid as well with pressure differentials.

Also there's no way the bones actually move that much?

Spinal fluid is especially pumped during sleep. Bones are especially malleable during sleep. Sleep posture is probably way more important than daily posture.