Place sliced tomatoes in a single layer on a cooling rack placed over the sink or baking sheet. Sprinkle with kosher salt. Let drain for 30 minutes. Flip tomatoes slices over and repeat.
Place sliced onions and butter in a small skillet over medium heat. Add thyme sprigs.
Cook onions, stirring occasionally, until nicely browned and caramelized.
Prepare a 9 inch baking dish by spraying with non-stick spray.
Remove thyme stems from onion. Place caramelized onions in the bottom of the prepared baking dish.
Layer half the yellow squash and lightly sprinkle with 4-1-1 seasoning.
Layer half the zucchini and lightly sprinkle with seasoning.
Scatter half the peas over zucchini.
Layer half the tomatoes and top with half the basil.
Layer half the grated cheese.
Repeat with remainder of the ingredients.
Bake at 375 degrees for one hour.
Let sit for at least 15 minutes before serving.
Enjoy warm or room temperature.