Healthy Mac and Cheese

Caramelization of Onions
2 Melt the butter in a 10 inch cast iron skillet. Add 1/2 tbsp olive oil and heat it. Next, add the sliced onions, 3 sprigs thyme, bay leaves, grated garlic and stir.(Tip: More detailed steps for caramelizing onions here. I use the 7.5 mm setting on my mandolin slicer.)
3 Sauté for about [timer minutes=20]20 minutes[/timer] until nicely caramelized, checking and stirring in between. Stir in a pinch of salt and pepper. Transfer the onions to a separate plate and set aside.
Prepare Butternut Squash and Pasta
6 While the onions are caramelizing, bring 4 quarts of salted water to a rolling boil. Add the chopped butternut squash and cook for [timer minutes=5]5 to 6 minutes[/timer] until tender. Using a slotted wide spoon transfer the cooked butternut squash to a high speed blender and set aside.
7 In the same boiling water add the lentil pasta and let it cook for about [timer minutes=3]3 to 4 minutes[/timer] (2 minutes less than al dente stage, as it will cook while baking later).
8 Drain the pasta and transfer to a bowl and toss it with some olive oil to coat the pasta. Spread the pasta over a plate to let it cool completely. This will prevent clumping.
Cheese Sauce and Assembly
11 Preheat the oven to 375 degrees F.
12 Add milk and 1/2 tsp salt to the butternut squash in a high speed blender and puree it to a smooth paste. If you dip a spatula into the mixture and run a finger over, it should leave the impression.
13 Pour the butternut squash and milk mixture into the cast iron skillet and heat it at medium setting for about [timer minutes=5]5 minutes[/timer]. Stir half the caramelized onions into the sauce. Adjust the salt to taste.(Tip: If you prefer, you can also try adding the caramelized onions while blending the squash and milk mixture. But the onions are so well done that you may not need to)
14 Move the skillet away from the stove, add the cheese to the sauce, reserving a little for topping in the end. Stir the cheese into the sauce as it melts.
15 Then add the cooled pasta and any optional seasonings to the sauce and stir. Add dollops of the remaining caramelized onions on the top and tuck it in lightly using a fork.
16 Top with the remaining shredded cheese. And then with gluten-free breadcrumbs and Parmesan cheese if you prefer.
17 Place the skillet, uncovered in the oven and bake it for [timer minutes=15]15 to 20 minutes[/timer], until golden brown on the top (or just broil it a couple minutes more if the top doesn't turn golden).
18 Serve it hot and fresh from the oven. Scatter a few thyme leaves on the top if you prefer.
Stove Top and Broiled Version (Optional)
21 Alternatively you can just broil the top for a few minutes until it is golden brown on the top and skip the baking. You may want to cook the sauce a bit thicker before adding to the pasta as well.