Dropouts and poor academics should indeed count against the APR, no doubt, because they demonstrate at least a degree of culpability on part of the athletic department for not encouraging the student athlete to hit the books or stay in school. However, transferring to another university (where their education will continue) and leaving early for the NBA (a great employment opportunity, and preparing students for gameful employment is a main focus of a college education) should not.
If a student athlete screws off academically or drops out while on scholarship then sure, the school should get some blame. However, going to another school--for whatever reason--or declaring for a professional in which your scholarship is being paid, should not.