Salt the eggplant: lay slices on a rack or paper towels. Sprinkle both sides lightly with sea salt. Let rest 20 minutes. The salt draws out moisture - you will see droplets form on the surface. Rinse well and pat completely dry with paper towels. Dry eggplant is the difference between a crunchy crust and a soggy one.
Make the tomato sauce: heat olive oil in a saucepan over medium heat. Add garlic and cook 1-2 minutes until fragrant - do not brown. Add crushed tomatoes with juices, thyme, oregano, and red pepper flakes if using. Simmer uncovered over low heat 20 minutes until slightly thickened. Season with salt and pepper. Set aside on low heat.
Set up your breading station: beaten eggs in one shallow bowl, Parmesan mixed with almond flour, garlic powder, oregano, paprika, and black pepper in a second bowl.
Dip each eggplant slice in egg, letting excess drip off. Press firmly into the parmesan mixture on both sides, making sure the crust adheres completely. The parmesan needs pressure to stick - press it in with your fingers.
Preheat air fryer to 400F. Spray basket generously with avocado oil. Working in batches, air fry eggplant slices in a single layer for 6-7 minutes, flip carefully, spray the tops, and cook another 5-6 minutes until deeply golden and crunchy. Do not crowd the basket or the slices steam instead of crisping.
Build the stacks immediately while the eggplant is hot: place one slice on a flat surface, lay one round of fresh mozzarella in the center, and top with a second slice. Press gently. The residual heat will begin melting the mozzarella within 2 minutes.
Spoon warm tomato sauce onto each plate. Place 2 stacks per plate on top of the sauce. Finish with torn fresh basil and a drizzle of extra-virgin olive oil.