I think you're right! My last physical therapist was a sports medicine guy who worked mostly on athletes, and he seemed convinced that the issue was just "muscle imbalance" in my scapula and shoulder. He kept telling me that it was all about strengthening the counterbalancing muscles, but he never addressed the fact that my neck and trapezius were just getting more and more tender the more exercises I did, even if it WAS improving some kind of muscle imbalance. Actually, one issue with that might just be a trigger point in my pectoralis, because that's what seems to be "winging" my scapula and shoulder to an extent. It's also giving me some dysfunction/pain in the collar bone in the AC and SC joint areas. Unfortunately with that I think I just have to leave it alone or else it will get worse! So I bet you're totally right that these trigger points need to be addressed first. It's just so hard when things are seized up, especially in the scalene area, which seems to be least amenable to TrP therapy so far (and why I wanted to look into Botox).

I think the next PT I go to will have to be someone who is aware of the importance of releasing these trigger points with some manual technique. The PT I had before my last guy was much better, and I remember feeling a lot of relief when she gently held her finger on some crucial muscle area, and I felt the tension gradually melt away a bit (but only after she had her finger on there for about a minute).