For Medicare / Medicaid patients, CMS guidelines supercede other guidelines. They spell out exactly what they want and since they hold all the money, and can implement all the laws, they are the one's carrying the big stick.
For non medicare payers, AMA for CPT, Coding Clinic (AHA) for ICD-9 should be the rules. If a private payer publishes their rules, and a physician agrees to participate with that payer, they have agreed to "play" by their rules.
The problem lies with the private payers that do not publish their rules, do not follow AMA or AHA or even CMS
Also, keep in mind that the Kennedy Kassabaum bill gave the federal government the authority to prosecute physicians under the federal fraud statutes, claims of fraud in dealing with private payers even when the rules with them are not very well defined. For example, a physician can be accused of unbundling, but what is unbundling when the private payer does not publish their bundling rules (they are propietary) and the physician only has access to CMS's NCCI (there are no bundling rules from the Coding authorities ie: AMA and AHA). It becomes a very fine line that is walked.
For the sake of the CPC credentialling exam, the AMA rules for CPT coding and the rules spelled out in your ICD-9 manual are the only guidelines and rules you are being tested on. You are not tested on reimbursement, medicare , cms or any other guidelines.
I hope this was of some help.