When doing an examination, one of the goals is to determine the source of the pain or mobility restriction, even though it is not the most important issue. My professional development courses come from a variety of sources and, thus, have different beliefs. Your more traditional manipulative courses believe the origin of all issues comes from the joint. Your myofascial type courses believe the origin is muscular. Typically, we see theses two things occur simultaneously. If you take a look at the spine, for example, you will often see "tender points" at the same level as a hypomobile joint. Which is causing which? If you treat either, usually the other will improve as well.
Personally, I think it is advantageous to include the muscular and joint-based assessment and treatment techniques. Having recently taken a dry needling course, I am recognizing muscle referral patterns I would have previously quickly ran to the spine for diagnosis. While there is likely a link between the two, it may be beneficial to know both the muscular and joint-based involvement. A true muscular referral or radicular referral pattern likely will respond better when the true pain source is treated (as well as the cause).