Bosses usually have more hp and damage output than the player(s) do, sometimes by a large amount. And in certain cases (like pokemon) the player has to face multiple of them in a row, like the elite four, the boss gets to fight them fresh while the player doesn't have that option. Healing is the player's answer to this difference, so they can fight on more even footing.

Also the boss healing basically takes all the hard work the players did to whittle it's hp down and chucks it out the window.

Look, when the damage cap is 9999 hp, the player hp cap is 9999 hp, and just to be cheeky the boss has 50,000,000 hp; healing makes one side of the equation be behind less and one side of the equation cheat more.