Good question, Craig.
Structural balance is used more in making sure your system is structured optimaly for your efforts, and it is one stage above an imbalance that created an injury. For example your rotator cuff should be a certain percentage of your close grip BP in order to advance optimaly in your efforts to increase your bench. If you dont reach that certain percentage, it doesnt mean you will automaticly injure yourself, most times, the body will protect itself by not letting you bench more weight.
Now when an imbalance is more drastic, it can cause an injury. Then i wouldnt go directly the structural balance root, but would try to bring the system up to par together, while supplementing the compund work with special isolation movements according to your needs of the athlete. For example, I would rehab a torn ACL with some sled work and advance into squating, while maybe using some isolation movements for the hamstrings because of the problematic requiretment patterns of the hams after ACL tears. After I'll bring the athlete back to normal strength levels and ROM and I would want to take him further I would go the structural balance root. Structural balance is a way to tinker with your system and make it better - similar to those happy souls that geneticly have the right balance between various muscles and due to this fact just keep on advancing using compund movments only. If you are satisfied with your gains, no prob. But if you feel they are less than optimal, try the structural balance test, correct deficiencies and fly away. It is my experience from the last 6 years that SB works big time.