I'm skeptical about the idea of cracking either causing or relieving headaches.

How have other possible causes been ruled out?

There is a logical fallacy known as "post hoc ergo propter hoc" which means "after this therefore because of this."

Just because Y follows X, does not mean that X causes Y.

The fact that it is natural means nothing. Kratom can cause addiction. It is active at opioid receptors

Morphine occurs in nature!

Diaceytlmorphine (heroin) is simply a prodrug of morphine. Diacetlymorphine is so close to morphine that it is often referred to as a "semi-synthetic" opioid.

Another problem with kratom is you don't know how much of the active ingredients you are getting.
The active ingredients are mitragynine and 7-hydroxymitragynine, which are (partial) agonists at the mu- opioid receptor. At least with a prescription drug, one can measure their dose.

There is no reason to assume that "natural" implies "safer."

Kratom stops opioid withdrawal because it is substituting as an opioid.