Melt butter in a large Dutch oven over medium until sizzling. Add onions, bay leaves, thyme sprigs, salt, and pepper; stir to coat onions in butter mixture. Cover and cook, stirring occasionally, until onions are translucent and have cooked down to about half of their original volume, 20 to 25 minutes. Uncover and cook, stirring occasionally, until most of the liquid has evaporated and onions begin to stick to bottom of Dutch oven, 35 to 40 minutes. Cook, stirring often with a wooden spoon to scrape up any browned bits and adding splashes of water to deglaze the bottom of the pan, until onions are jammy and deeply browned, about 40 minutes.

While onions cook, roast poblano chiles, 1 at a time, over a medium gas flame, turning with tongs occasionally, until blackened all over, 10 to 12 minutes. Place charred chiles in a small bowl, and cover with plastic wrap. Let steam 10 minutes. Rub charred skin off chiles; discard skin. Cut chiles in half; remove and discard seeds. Slice chile halves into thin strips; set aside.

Preheat oven to 400°F. Stir balsamic vinegar into onion mixture. Reduce heat to medium-low, and cook, stirring often, until onions have absorbed vinegar and look dry, about 5 minutes. While onions cook, remove and discard bay leaves and thymes prigs. Dust onion mixture with flour, and cook, stirring often, 10 minutes, adding about 2 tablespoons water at a time as needed to scrape up any browned bits. Stir in chicken broth, and bring to a vigorous simmer over medium-high. Reduce heat to medium-low, and simmer, stirring occasionally, to allow flavors to meld, about 10 minutes. Turn off heat; stir in roasted poblano strips. Season with salt to taste.

Divide soup evenly among 6 ovenproof bowls, and place on a large rimmed baking sheet. Top each bowl with 2 baguette slices and 1/3 cup cheese. Bake in preheated oven until cheese is melted, about 8 minutes. Garnish with microgreens or cilantro, if desired.