All cocoa seeds are ferented naturally for a few days after they are picked to make them edible. They are then broken into nibs, roasted and and then ground into cocoa powder and butter. The cocoa power is often then dutched (mixed with alkali) to make it less acidic.

All this processing probably has as much effect on antinutrients in the cocoa as you are going to get. Anything else you try to do yourself would be more likely to just make it unappetizing in my opinion. Roasting probably reduces the phytates so you could avoid raw cocoa or chocolate.

Just enjoy your cocoa and chocolate for what it is, you are unlikely to eat enough for the phytates, oxalates etc to have any effect on your health.