Preheat the oven to 350 degrees F. Line a baking sheet with parchment paper.
Heat a large skillet with a lid over medium-high heat and add the bacon. Cook, stirring occasionally, until the bacon is golden brown, about 9 minutes. Transfer the bacon to a plate using a slotted spoon. Add the onions to the skillet and cook, covered, stirring occasionally and scraping up the stuck bits on the bottom of the pan as needed, until the onions release their juices and are caramelized, golden and soft, about 30 minutes. (If the onions begin to brown before they soften, stir in a tablespoon water, lower the heat and return to cooking.)
Combine the butter, thyme, 1 teaspoon salt and some pepper in a medium bowl. Stir in the onions until the butter melts and becomes saucy.
Meanwhile, with a large serrated knife, shave 1/4 inch off the bottom crust of the bread.. Make 1-inch wide crosshatch cuts on the top of the bread, three-quarters of the way through to the bottom. Put the bread on the prepared baking sheet.
Spoon 3/4 of the onion mixture into all of the slits. Mix together the Gouda and mozzarella in a small bowl, then stuff three-quarters of the cheese inside all of the slits. Spoon the remaining onion mixture on top, followed by the remaining cheese. (The bread will be very stuffed and messy.) Cover the bread loosely with foil and bake until the filling is warm and the cheese is melted, about 25 minutes. Transfer to a platter or cutting board and top with the bacon and parsley. Serve immediately.
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