Crossfit is ok as a general conditioning tool. In fact, they have some good things in their program and they are always learning (they are usually the first to purchase my DVD's or any new product I put out) But their program is not meant to be specific to baseball.
I have no doubt your son has made improvements while following and it's certainly a good idea to add in some baseball specific movements, but that is precisely my point, you have to add in additional work to make it specific to baseball, which was the initial question that was asked of me.
The main thing I don't like about Crossfit is the extremely high repetition of certain high motor patterns movements (such as power clean and power snatch) with almost zero regard to technique. You can only do som emany reps in these exercises (typically 3-5 for higest benefit), yet on certain Crossfit workouts they recommend upwards of 25-50 for 1 set, which will certainly cause mechanical breakdown and lead to injury.
I know plenty of people to have followed Crossfit and they have all stopped for 1 of 2 reasons:
1. It's too hard - Most simply do not want to train hard - and I do give Crossfit credit for this
2. They get hurt - Crossfit, in my experience, has a high rate of injury due to what I touched on above.
However, I always recommend someone to follow a program they have found works well for them. I wish the best for your son.
As far as UC Irvine I cannot speak for that because I have not reviewed their program. But as a consultant to dozens of NCAA programs I can tell you first hand more often than not the S & C program is a mess. Thta is precisely why they hire me to come in a provide an overhaul. Now I'm not saying this is the case with UC Irvine, just that because one NCAA schol follows something does not mean its the best.
However, I wouldn't think a S & C coach would need to follow a generic plan such as Crossfit, so that is a bit alarming if in deed that is the case.