Bring a small pot of water to a boil. Slice potatoes in half, then cook in boiling water for 5 minutes. Drain and let cool, then slice thinly. While potatoes are cooling, slice the rest of the vegetables.
In a large saucepan, combine the butter and flour on low heat for a couple minutes. Microwave milk for 1 to 2 minutes until hot. Slowly pour milk into the butter and flour mixture while stirring to avoid any lumps. Stir mixture on medium-low heat for another 3-5 minutes until it coats the back of your spoon. Add in a pinch of nutmeg, take off heat and set aside.
Preheat the oven to 375°F. In a large deep round dish, pour in the jar of marinara. Sprinkle in some salt, pepper, red pepper flakes and half the thyme leaves. Drizzle a tablespoon of olive oil. Then pour béchamel sauce in a swirl. Mix it in just a little.
Add the veggies in layers on their side going in a circle. Do one slice of each veggie and repeat.* Once the dish is filled, drizzle olive oil, remaining thyme, salt and some red pepper flakes. Cook for 55 minutes to 1 hour. If the tops of the veggies are browning too much, put a round of parchment or aluminum foil on top.
*If you have leftover veggies, saute them in a pan with some salt and red pepper flakes and use them as a side for another meal.