In the bowl of a food processor or a blender, combine cilantro, garlic, jalapeno, lime juice, salt and pepper. Pulse to roughly chop. With the motor running, slowly pour in the olive oil. Blend until smooth.
The Ppizza:
Preheat the broiler. Set the rack 2 to 3 inches from the heat source.
Lay the eggplant pieces on a baking sheet lined with foil. Brush both sides of eggplant with olive oil and season with salt and pepper.
Place eggplant under the broiler and cook until golden brown, 2 to 3 minutes per side. Watch it carefully so it doesn't burn! Let cool on baking sheet for about 5 minutes.
Lower the oven rack to the middle setting and turn the oven to 425 degrees F. Place the naan pieces on an ungreased baking sheet.
Divide the pesto between the pieces of naan and spread evenly. Top with eggplant, overlapping the pieces slightly. Sprinkle with dried red chile flakes and top with mozzarella.
Place the pizzas in the oven and cook until cheese is melted and naan are starting to brown, 8 to 10 minutes. Remove from the oven and let rest for about 5 minutes. Cut into strips and serve.