It is true that >50% of applicants don't get admission to any medical school.
At some schools, there are 100-150 seats and >5,000 applications meaning that 2-3% of the applicants end up being students at that particular school.
However, keep in mind that many schools make offers to 2-3 times as many applicants as there are seats. This is because some of the top applicants get into more than one school but can attend only one school.
The schools tend to provide average (median or mean) GPA and MCAT for its newest class of students. These students are also called matriculants.
AMCAS publishes the average and 10th and 90th percentiles for accepted applicants. This tends to be higher than the average for matriculants because just as the OP observed, an applicant with a 40/4.0 who is admitted to 5 dfferent schools gets counted in all 5 as an admitted applicant but will be counted at only one school in terms of matriculants.