Academically qualified means that the admissions committee has reviewed the academic components of the candidate file (grades, test scores, academic evaluations, school profile, etc.) and answered yes to the following question: Does this candidate possess at least the minimum skill necessary to handle the academic program at West Point?
A seemingly low score in a particular area is not necessarily a deal breaker. A comparatively low GPA in a very rigorous program may be viewed more favorably than a high GPA in a mediocre program. Real life example: Several years ago a candidate ranked near the bottom of the high school class. Very bad at first glance. However, the school was a small private school that sent virtually all students to Ivy League and similarly elite colleges. Also, excellent test scores and a rigorous curriculum confirmed that the low class rank was not a relevant data point.
While most candidates fit into the norm and can be accurately assessed by standard criteria, West Point is not going to lose an outstanding candidate because their preparatory program is outside the norm.