Well I can tell you from looking through the process for my son, what qualifies without question from the Clearinghouse for the core classes is pretty well known in the Klein district (they are specifically listed by the NCAA - there are probably over a hundred kids in the district every year that receive athletic scholarships). It is when you try to pass off classes they haven't reviewed before or slip in a non-college prep math class that you get into trouble. If you did Algebra I, Geometry, Algebra II you would have zero problems. I would surmise that he has a non-standard class and the NCAA puts those at the bottom of the pile. Don't blame the NCAA, it has to come down to the school counselors, HS Coach and the kid. He has been known to be a prospect for a long time, and this should have all been in order. From a fairness perspective, there is no reason to jump him to the front of the line because he is a big time prospect and a football player. Why should he jump ahead of a female soccer player in the review queue for vetting non-standard classes?
IMO, if it is truly one math class at issue, he will not go JUCO. That would be foolish; he can take a class this fall (at the HS?) and enroll in January. And if gets approved anyway but misses fall camp, he might as well wait to enroll in the spring and effectively "gray shirt".