The real world piece that is missing is that if an Academy player doesn't fit your plans (wrong position, team full of better players, player would rather play somewhere else [which isn't a problem in the game]), a real world team can sell the players negotiating rights. That is not possible in the game unless you first sign the player to a pro contact and spend the tokens.
The Dev's justify the tokens (both for transfers and U21 signings) as "Managerial Influence" required to retain a player. It makes a certain amount of sense, except for the fact that an Academy player is already that club's property. Maybe you don't have the "Influence" to keep the player, but the asset is being taken away with no compensation to the club for developing the player. That doesn't happen in the real world.
For unsigned U21 players, managers should either get cash back for the players sale, a token kick back (either a percentage of the tokens used in the transfer or a fixed 3-5T "development fee" depending on the skill of the player), or be able to sell the player on the direct player transfer market with their friends.