To unlock the Otka Island Maze you first need to obtain the Sol Blade from the Apollo Sanctum. Sail from Tonfon to the west until you see a small island surrounded by rocks, wait until you see the whirlpool and sail right into it. You will end up on the other side of the rocks with the island. Land then go inside and then go to the door. Select it to initiate text then go to your inventory and use the Sol Blade. The Maze holds the Summon Catastrophe and extra boss Ancient Devil.
In order to access the final optional dungeon you need to beat the final boss and save your game after the credits roll. Reload your game and sail south from Tonfon and eventually you will reach a sea shaped peninsula at the edge of the world. There will be a whirlpool in that location if you have beaten the final boss enter the whirlpool and sail east from the exit point to reach an island that has cave leading to the entrance of Crossbone Isle which is home to the hardest boss of Golden Sun Dark Dawn. Good Luck
To unlock the door in Burning Island Car that hold the Summon Daedalus and the extra boss(es) Ogre Titans, you first need to obtain the Sol Blade from the Apollo Sanctum. From Tonfon, sail all the way back to Burning Island Cave (volcanic island that has the counter clockwise swirling path to the top). Go to the bottom of the cave and go to the door which cannot be open before and the select it. After the text go into your inventory select the Sol Blade and use it.