Preheat oven to 450 degrees Fahrenheit. On two baking sheets, combine mushrooms, shallots, thyme, 1/2 cup olive oil, and salt and pepper to taste. Toss the mushroom mixture so that each piece is coated in oil and spread evenly across the pans. Roast the mushrooms, stirring them half way through cooking until browned and crisp, about 25-30 minutes.
Meanwhile, in a large sauce pot or medium-sized dutch oven, heat the remaining 2 tablespoons olive oil over medium heat. Add the onions, garlic, chili flakes, and season with salt and pepper. Cook until onions are soft and starting to look translucent, about 7 minutes. Add parmesan rind, bay leaf, beans, and bean broth. Using a vegetable peeler, zest one of the lemons, taking care to create large peels. Add this to the beans. Season with salt and pepper, and add enough water so that the beans are just covered.
Bring the beans to a full boil, and reduce to a simmer. Simmer the beans until the broth is deliciously creamy, about 35-40 minutes. Once the beans are done, remove lemon peels and parmesan rind. Use a microplane grater to zest the second lemon into the beans and add additional salt and pepper if needed. Stir gently to combine.
To serve, spoon beans and bean broth into shallow bowls. Top with cooked farro, crispy mushrooms, scallions, dill, and a squeeze of lemon juice. Grate parmesan over the top, adding a pinch of red pepper flakes and lots of cracked black pepper.