Preheat oven to 425℉. Place a piece of parchment on a baking tray for easy clean-up.
Take tomato slices, cut each in half, and then press gently between paper towels to absorb extra liquid. Set aside.
Cut each squash in half lengthwise. On the skin-side of each half, cut a slice to form a level base so that they don’t tip when baking.
Place squash halves, skin-side down, on baking tray. Brush flesh of each with olive oil and sprinkle with salt, pepper, and garlic powder.
Cut each cheese slice in half so they better fit on squash. Place two cheese halves on each squash followed by two tomato halves. Sprinkle oregano, rosemary, chives, thyme, and fennel seeds evenly over the squash. Finish each with a sprinkle of red pepper flakes and parmesan cheese.
Bake for 10-15 minutes, checking for doneness by poking with fork. Remove from oven and top each squash slice with shredded basil and a drizzle of balsamic before serving. Serve warm.