Nate,
In nonpathological situations, athletes recruit the TVA reflexively. If it didn't you would never be able to throw a ball, run, jump or whatever because you would fall over. It is not something that needs to be taught. Also realize that the lumbar musculature and peripheral stability plays much greater role in stability than the TVA. The research that Clark, Chek, Santana, Gambetta, and many others promoting functional training came from subjects with back pain and other pathologies (heavily referencing Richardson, Jull, et al.). Also, Jandas research (which also forms a basis for their conjectures) has never been substantiated to acceptible levels in the scientific community. There is some great info on this on the Supertraining board at yahoo.com if you are willing to challenge your current beliefs and perhaps shed some light on topics you may be interested in.
Take a healthy well-trained running back and put him on a wobble board and he will wobble a great deal if he has never done it before. Does that mean he lacks proprioception? No, it means he lacks the skill to balance on a wobble board. Once he learns to do a blindfolded, single-leg squat on a wobble board does that mean he now has better proprioception for his sport No, it means his skill has improved in a blindfolded, single-leg squat on a wobble board. Most of the so-called proprioceptive exercises are specific skills in and of themselves. They require learning, not increased proprioception. Your proprioception does not increase when learning a skill (It’s actually at a fixed level from a neurologic standpoint, again, in not pathological situations) but intermuscular coordination does improve specifically for the new task/skill.
Muscle imbalances assessed in clinic with static or passive methods do not necessarily apply to dynamic situations. A lengthened muscle in static posture (rhomboid for example) is not necessarily weak dynamically and there is no evidence that strengthening it will improve posture (there is research demonstrating this that functional training proponents are ignoring for some reason). Tight muscles are not necessarily facilitated, especially in dynamic situations. There is a very low correlation between static and dynamic flexibility (r=0.62). Of course you will have athletes with flexibility issues, but that does not imply muscles imbalance as there are very few true antagonistic muscles (one muscle never functions alone and almost all muscles at one time or another function as prime movers, stabilizers, fixators, co-agonists, etc.). Again this is one of the drawbacks of Janda's research which gets passed on as gospel (and very heavily criticized in the scientific literature).
Your quote:
"specific training is fine for a sport but if an athlete is landing wrong, pushing off wrong, turning wrong or even slowly due to overactive synergists, inhibition or a weak core.....now what? just keep practicing and getting stronger in the wrong ways?"
You are describing issues of lack of skill and intermuscular coordination. That is what coaches do. Teach skills. Some coaches are better than others. Some athletes lack the abilities to develop that skill. Before you could throw a ball well was it because you had an overactive synergist and muscle imbalance? Or was it because you had not yet developed the intermuscular coordination to throw well? How did you get better at throwing? A swiss ball, pec minor stretches, and scapular retractions? No you kept throwing the ball. Your Dad said do it this way. Your coach said do it this way and you learned the skill of throwing with greater proficiency (intermuscular coordination).
I was right where you are several years ago. It can get confusing at times. Keep reading on motor control theory, biomechanics, etc., and question it all regardless of the source. Never accept anything as absolute as I am sure there are exceptional situations to which the above may not apply (I try to keep learning as well)