First, all players get paid on perceived value. Edwin Diaz just injured himself and is out for the season. Is that "fair"?
It matters a lot if the top players say to hell with it, play independent ball for a year and sign big free agent contracts with the Yankees and Dodgers when their draft rights expire. It matters if players drafted by the Pirates (knowing their pay is the same no matter when they get drafted) decide to go back to school for a year and re-enter the draft hoping some other organization drafts them instead. It makes the draft pointless. That would kill the main way small market teams acquire talent.