Prepare salsa by combining all ingredients in a small bowl; stir and set aside.
Preheat oven to 375°F.
Slice the eggplants in half lengthwise, right through the stem. Carve into the eggplant flesh all the way around the perimeter, and scoop flesh out; set aside. Place eggplant halves on a baking sheet, facing up. Brush the eggplant halves with 1 Tbsp. of the olive oil and lightly season with salt. Bake eggplant for 20 minutes, or until golden brown and lightly tender.
Heat remaining 2 Tbsp. oil in a large skillet over medium heat. Finely chop eggplant flesh and add to skillet, along with shallots and garlic. Cook mixture for 5 minutes, stirring occasionally, until softened. Stir in quinoa, tahini, balsamic, and herbs; cook 2 to 3 more minutes, stirring often, until mixture is warmed through. Season to taste with salt and pepper.
Remove eggplant boats from oven and divide quinoa mixture evenly into each boat. Top with Mediterranean Salsa.