In a medium bowl, vigorously whisk the whole eggs, egg whites, sea salt, and black pepper for at least 60 seconds until the mixture is very frothy and aerated.
Place a medium non-stick skillet over medium-low heat and add the ghee, swirling to coat the bottom of the pan.
Add the baby spinach to the skillet and sauté for 1-2 minutes until just wilted, then remove the spinach from the pan and set it aside on a small plate.
Pour the egg mixture into the same skillet, keeping the heat at medium-low to ensure a tender texture without browning.
As the edges begin to set, use a silicone spatula to gently lift the edges and let the raw egg flow underneath.
When the top is mostly set but still slightly moist, sprinkle the cheddar, feta, and parmesan cheese evenly over one half of the omelette, then top with the sautéed spinach.
Carefully fold the other half of the omelette over the filling and let it sit for another 30-60 seconds until the cheese is gooey and melted.
Slide the omelette onto a plate and garnish with finely chopped fresh chives before serving.