Each community has a different set of challenges that it must overcome in order to be a good, productive Stack Exchange site, which is why the guidelines in the FAQ are guidelines as opposed to strict rules written in stone.
While the goal of Stack Exchange is to be a resource of knowledge for years to come by focusing on high quality questions and answers, getting to this point involves interpreting and applying those guidelines somewhat differently in different communities.
For instance, the Skeptics SE community decided that they would enforce a strict interpretation of Good Subjective, Bad Subjective where each answer must be backed up with several sources. Other Stack Exchange sites, like Stack Overflow, pretty much avoid subjectivity completely, while Project Management Stack Exchange has a very laid back approach to this particular guideline.
If the Stack Exchange Community Managers feel that the site isn't producing high quality questions and answers, then they'll suggest the community take a different approach, but not being experts in the topic, the moderators are appointed to help the communities work through their issues so that they can become a productive Stack Exchange Q&A site.
In short, a community's rules are its own; however, they should be created within the spirit of what Stack Exchange stands for, which is to make the Internet a better place by focusing on high quality Q&A.