The best way to look at these stats is what is the average strength of schedule of a team that a Major team plays?
What is the average strength of schedule of a 'AA' teams opponents?
What is the average strength of schedule of an 'A' teams opponents?
What you will find is the Major player play much tougher competition than Conference 'AA' or 'A' players play on average. So its the 'A' and sometimes 'AA' players that have more of a chance to "pad" their stats if you want to call it that than a Major player that is playing against other Major teams pitching and defenses more often.
Great discussion though.