Apparently it's so players can't dictate where they'll be drafted by saying "If the Braves draft me, I won't sign and thus go to school unless you trade the pick."
Players still have that leverage to some degree (at least high school players), but MLB doesn't want a lot of trading due to signability concerns.
I think it has more to do with the fact that every organization has an entire minor league system to fill. It's sort of a way to ensure a team doesn't trade all their picks and leave their low minors screwed.
Also, I don't think they want a team to be able to add so much in pool money they can just dictate all the top players they want.