Well, I never thought I'd be defending chiropracty, but here I am. I agree with some of what you are saying, but you need to consider the interactions between muscle, nerves, and bone. These interrelated elements can interact and feed off of each other, sometimes chronically, during a structural dysfunction, caused by trauma or by defect. Bones don't exist in isolation; when structure is out of place, as you say, it will impact your muscle and nerves, and these, in term, will impact your structure. It's a bit of a positive feedback loop, sometimes involving reflexes. Also, let's not forget local inflammation and it's associated effects. This sequence often results in the obvious muscular, structural, and even neurological signs that we note upon physical examination (restrictions and loss in the range of motion of a joint, diminished muscle strength and reflexes, displacement of bony structures, tissue texture changes, asymmetries, etc.), but also the less quantifiable and specific symptom of pain. There is often the question of which came first and often we don't know. However, if you make a structural or muscular adjustment, you can stop the vicious cycle and hopefully provide some relief for the patient's pain and encourage healing. I'd say that such manual interventions are more like adjuvants than primary therapies.
While it's true that there are pathologies that can't be fixed by manual intervention, a tangible example of where manual therapy can perhaps help "fix" a dysfunction is when you have a severe somatic dysfunction, let's say, of your spine at T5-9, for example. There can be spinal nerve compression at that level that leads to not just local pain (back pain), but a viscerosomatic reflex response, and possible pain and dysfunction at other associated sites, too. You relieve the compression/dysfunction through some muscle energy and HVLA and you could potentially help solve your patient's pain and other potential problems, in conjunction with other modalities, of course. Now, of course, we need to look at what exactly was the root of the patient's spinal dysfunction. Maybe it was a short leg, dysfunctional posture, innominate dysfunction, trauma, or the like. Maybe it has to do with tight muscles or repetitive stress injuries. You take it all into account and consider patient education as well, all in conjunction with conventional and manipulative therapies.
Perhaps even more tangible are gross joint dislocations and neuropathies that are the result of bone displacement and/or muscle/fascial tightness, or the like. You can create very dramatic results with the right type of manual intervention in these cases.
Anyway, I need to get back to studying, but what I'm trying to say is that you should try to look at the whole picture and before throwing the baby out with the bath water.