If I remember correctly, the optional super boss in the final dungeon drops an all-powerful weapon, so it's only "sportsmanlike" to make the final boss battle more difficult for those wielding this weapon. Of course, the developer would put the cherry on the cake if the game's story could even logically explain the final boss's boost.

I think that more games should be designed this way when it comes to the power relation between final boss and optional super boss. Since the latter is usually the stronger one, too many players that defeated the optional super boss complain about the final boss being "too easy". I'm sure that diligent players won't be punished. Fighting against the boosted version of the final boss while wielding the all-powerful weapon dropped by the optional super boss should still be easier than fighting the non-boosted version of the final boss without this weapon.

Finally, it's Ephiam's decision, even if he negates everything I've written. ;)