I would also encourage you to look into someone who does the McKenzie approach.

McKenzie doesn't work for everyone, but it does sound like it would be a good one for you.

Ultimately, everyone moves differently and we all have movement/muscle imbalances because of our habits. But treating them comes down to figuring out what movements ease your signs and symptoms and what movements make them worse and working with those to increase strength and function. Honestly, I never want my patients to be in more pain after their treatments, tired and fatigued sure, but not more pain. If the exercises are aggravating your back pain, you will move incorrectly to try to protect your back or compensate and that won't help you recover. So even if your PT is on the right track, it would be highly recommended that they find exercises for you that achieve the goals in terms of strengthening and regaining motion, without causing you pain.