There are a number of professional leagues that produce major league caliber players. Leagues in Puerto Rico, the Caribbean in general, Mexico, Central and South America, Japan, Taiwan and Korea all produce significant numbers of MLB quality players. Those leagues, however, are not on a par with MLB. The Negro leagues fall into this category.
When we're talking about top tier athletes of any stripe the differences between "major league" and "other" are generally measured in hundredths of a second, one hit a week, ability to maintain that mental edge for a couple of seconds longer than the other guy, etc. In that regard the secondary leagues simply can't compete with the major leagues. They don't have the resources to do so. My grandfather used to complain about this kind of thing all the time. He had a jazz orchestra in Manhattan in the 40s and he constantly complained that as soon as he picked up someone "next level" along would come Basie or Goodman or Dorsey and off that talent would go. Sports leagues have the same issues and because of that your top players in the second tier leagues are constantly playing more games against third tier players and that boosts their stats.
Besides all that, Baseball has two primary components. The first is the statistical component. The part that can be measured is hugely important. The other major component, however, is the mythical or "what if" component. That's every bit as big as the statistical component because the nature of competition is that there is never a "best", there is only a "best at this time and under these circumstances". The AL and NL have a long history of statistics while the Negro leagues have a long history of "what if". MLB NEEDS that "what if" factor standing next to it just so its head doesn't get too big and it doesn't get too full of itself.