Doctors and therapists know that pain can be referred from somewhere else. This could be the result of nerve root irritation in the neck. Such a condition is called cervical radiculopathy.
If tender spots in the neck, shoulder blade (scapula), or arm are referred from the cervical spine, then treatment must address the problem. In this case, the spine should be the focus of treatment and not the tender spots.
Anytime muscles are tender or sore from cervical radiculopathy, other tests can be done to confirm the therapist's suspicions. Ask your therapist to explain his reasons for treating the neck. You'll likely find out the results of these tests.