Salt eggplant and let drain on a kitchen towel for 20 minutes; press off excess liquid.
Bring a pot of water to a boil. Score the tomatoes on the bottom with an X and blanch them for 30 seconds; cold shock and peel. Seed the tomatoes and finely chop. (You may also use canned tomatoes, drained and hand crushed if you prefer.). Reserve pot of blanching water to cook the pasta.
Heat 2 tablespoons oil, 2 turns of the pan, in a large skillet over medium-high heat. Cook eggplant until golden brown, about 10 minutes, remove and reserve. Add another tablespoon of oil to pan and toast breadcrumbs to golden; remove and reserve.
Add nuts to the skillet to toast; remove and reserve in large serving bowl.
Add final tablespoon olive oil and garlic, and stir 30 seconds. Add chopped tomatoes and season with thyme, salt and pepper. Stir 2 minutes.
Add tomatoes and garlic to almonds and combine. Cool to room temperature then stir in chili flakes, basil and EVOO, about 1/4 cup.
Turn the heat back on under the pot of blanching water. Salt water and cook pasta to al dente, reserve 1/2 cup starchy cooking water and add to pesto. Drain pasta and toss with pesto.
Arrange the eggplant in shallow bowls and top with pasta. Combine cheese and breadcrumbs and sprinkle over pasta to serve.