Depends on the college. It may be acceptable to UVA and engineering schools; it’s less acceptable at the HYP level, STEM kid or not. Particularly when its 2 years vs 4. 3 years they are more likely to get a little leeway.
Scheduling issues are always an acceptable excuse, unless the scheduling issue is a result of doubling or tripling up another core subject.
But getting back to this kid. UVA has a fairly onerous foreign language requirement to graduate. The more courses taken in HS, the fewer (potentially) courses he needs to take in college.