Place the cold water into a glass measuring cup and microwave on high for 3 minutes. While the water is heating, place the coconut milk into a small saucepan over medium heat. Whisk until combined, then add in the agar and salt. Whisk until it starts to bubble.
Remove the water from the microwave and whisk in the agar powder. Heat for another 30 seconds in the microwave, then remove and whisk in the agave. Set aside.
Lightly grease the inside of a Tovolo tray with a little coconut oil. Wipe away any clumps or excess oil. Using a tablespoon, place one spoonful of the coconut milk into each compartment. Drizzle any leftover mixture into the compartments evenly. Place into the freezer for about 10 minutes to slightly set.
Touch the tops of the coconut mixture gently with your fingertips. It should be slightly firm on the top, but soft underneath. If this texture is achieved, spoon the clear mixture into the compartments, leaving about a half an inch space at the top. Let it lightly set in the freezer for about 5 minutes, then remove and distribute the pomegranate seeds evenly into the compartments. Place it back into the freezer for 15-20 minutes, then transfer to the refrigerator to set for an additional hour.
To serve, place a plate, faceside down, over the top of the tray. Flip it over, then manipulate the tray slightly to release the cubes. Serve topped with some extra pomegranate seeds and lime zest.