I think this isn't specific to the Negro Leagues however. Baseball has always had variation and inconsistencies.
For example: You had ballpark configuration inconsistencies. Playing at the Polo Grounds or old Yankee Stadium meant that you weren't hitting a HR to center field. You Might get more extra base hits however. Ebbets field was the opposite. You could easily hit a HR to center, and if you were a lefty pull hitter, you feasted on the short RF porch.
You also had a significant dilution/loss of talent during the war years. Those stats are still valid too.
That said, I DO believe that he misperception that the Negro Leagues were loaded with Major League talent. Yes, there were a LOT of players that never got the opportunity to play in MLB due to disgraceful race policies, but the assume that every negro league player could have made it in MLB, if given the chance, is an assumption that I'm not willing to make and a lot of those Negro League teams were incredibly top heavy in talent, similar to MLB, as the stronger teams poached from the weaker ones, who had to sell to stay afloat.