Drain beans and place in a large heavy pot along with halved onion, Parmesan rind (if using), halved head of garlic, bay leaves, and 2 teaspoons salt. Add water to cover by 2″. Bring to a boil, reduce heat, and simmer until beans are tender, 11 1/2 hours. Meanwhile, cook bacon in a large skillet over medium heat, turning occasionally, until brown and most of fat has rendered, 810 minutes. Transfer to a plate with tongs or a slotted spoon. Add thinly sliced onion, shallot, thyme sprigs, and three-fourths of chopped garlic to pan drippings in skillet; season with salt and pepper. Cook, stirring occasionally, until onion is starting to caramelize and is very soft, 1015 minutes. Add wine, bring to a simmer, and cook, stirring occasionally, until liquid is almost completely evaporated, about 4 minutes. Remove from heat and pluck out thyme sprigs. Preheat oven to 400°. Drain beans, reserving cooking liquid. Transfer beans to a large bowl and mix in bacon, onion mixture, thyme leaves, and 1 1/22 cups cooking liquid (this will be most of it; mixture should be consistency of stew); season with salt and pepper. Transfer beans to a shallow 1 1/2-quart baking dish. Mix breadcrumbs, oil, and remaining chopped garlic in a medium bowl; season with salt and pepper. Scatter over beans; bake until liquid is thickened and bubbling and crumbs are golden brown, 4555 minutes. Let cool slightly before serving. Do ahead: Beans can be baked 5 days ahead. Let cool; cover and chill.