I know a few HS coaches that have a strong tendency... when they see 3/4, they want to take them all the way down to make them specialty guys. This has generally been an effective strategy. But, of course, arm health should always come first. Some make the adjustment with no issue, some do not. The transition should be introduced with some gradual ramping.
Many here will not agree with me but there is a difference between some soreness and pain. Pain is a clear indicator. Some soreness can occur when initially working back into a throwing routine, when throwing more than normal and when throwing in a different manner than normal (arm angle, etc.). A young HS player will benefit greatly from learning to differentiate. If in doubt, you are right to express concern. Questions should be asked and discussions regarding arm health (or health in general) are ones that are OK for parents to be involved in.
I know that is not as easy as it sounds. But only your son (and you) are close enough to the situation to make the determination. Hopefully, after concerns are expressed to the coach, there will be some more clarity.