2016,
I think it is important to know that there are multiple hitting mechanic philosophies even at the highest levels and things aren't always black and white right or wrong as many with strong opinions toward one or another would suggest.
So, be careful when you come here (or anywhere) for advice or confirmation on hitting instruction.
In the game swings, your son is certainly not chopping downward with his swing. In fact, once he gets the barrel to the zone, he is swinging slightly upward, which is fine. His balance, stance and load are well within the realm of what is typically taught. I could further analyze and debate what others are saying here. But I think the important thing is to come up with the best go-forward plan is for your son.
Understand that there are often adjustments made to swing mechanics and, yes, this will typically disrupt timing and consistent contact until the adjustment becomes more engrained.
I went to a college D1 game last weekend featuring a top 5 nationally ranked program. I noticed that this team had every hitter using a flatter-than-usual bat angle for their set and load position. It appeared that the coach was trying to simplify and eliminate unnecessary moving parts - more of a one-plane swing. My son played summer and scout ball with a few of these players and their swings looked quite different than they did a few years ago. Undoubtedly, they went through an adjustment process that took them a step or two back before progressing forward. Even though it looks a bit unorthodox as compared to today's more popular teaches, it's sure working for them now. Did I mention they are ranked top 5?
Where did your son learn the mechanics he is comfortable with? Does he understand the basic principals well enough to discuss? Does he understand the principals that the current coach is trying to convey? Is son open to learning new ideas and approaches? Can he have a discussion with the current coach to come up with a direction both will be comfortable with? Does your son understand that each coach he plays for will likely make some adjustments and he will need to continue to adapt? If there is a hitting coach (outside of HS) involved, can he help connect the dots between what is being taught? Does outside hitting coach know HS coach? I would explore intelligent discussion, open mind and communication as opposed to the "nod your head yes and then screw 'em" approach. That will generally not work well when it comes to developing relationships with his current and future coaches.