at least ranking between eras has generally the same universe of teams, games played, conditions of play, etc. there are a few differences in the ball over the years, but nothing like the differences between mlb and the negro leagues. and the pool of players for the negro leagues was much smaller. a lot of barnstorming more than a set league. not that there wasnt a set league for a lot of the history, but not for all of it.
i dont think the two leagues were equal and that the mlb pool of players was much deeper, but both leagues were diminished by the absence of the other league's great players.