Giving an example, something like the sternum is the location of the chapman's point for the pylorus. What's the rationale behind that? If we're talking some sort of nerve related cause, then dermatome wise I'd guess T6 or T7 and I would find it along some portion of that dermatomal segment. For somatic dysfunctions, why is the counterstrain point for a posterior C4 point extended, rotated away, sidebent away, but posterior C3 is flexed, rotated away, sidebent away? If you told me "Oh, it's because C3 articulates with the axis and the muscles attachments are different." But then why is a posterior C2 the same as a posterior C4. Complete head scratcher to me.
I don't know about Chapman's points and don't look forward to knowing about them, but in regards to CS this sort of stuff is beyond my knowledge of anatomy, but I wouldn't doubt that if you approached OMM faculty with that question they would certainly find the answer for it and the answer would certainly relate to the anatomy. The only time I ever go beyond the surface when studying anything is if going beyond the surface actually helps me remember better than just knowing an exception to the rule. In this case PC3 is only 1 of 2 exceptions in terms of treatment positions for the posterior cervical points. This is even easier to remember because its on the only cervical vertebra that has 2 designated points associated with it.
I was not implying that I correlate anatomy with OMM when i prepare for it (especially not to something as detailed to which muscles are associated with this counterstrain point or which muscles am I trying to engage in isometric contraction with MET). What I mean is that if I diagnose some dysfunction in the pelvis if the dysfunction is due to hypertonicity of some muscle groups attached to it then muscle energy would actually be a rational treatment especially if it has been demonstrated that isometric contractions alleviate hypertonicity. I don't really go beyond that because of the tendency for there to be lack of supporting evidence.
In any case if you feel like your understanding of anatomy is in conflict with OMM techniques, then that should just tell you to not bother associating the two things as a means of learning.