Preheat the oven to 400°F. Lightly coat a baking sheet with cooking spray. Gently remove the stems from the mushrooms and finely chop them. Arrange the mushroom caps on the prepared baking sheet.
In a medium skillet set over medium heat, melt the butter. Add the chopped mushroom stems and sauté, stirring frequently, until most of the moisture evaporates, about 5 minutes. Add the garlic and cook, stirring, for about 1 minute, until aromatic. Stir in the bread crumbs and continue to cook, stirring often, until they are lightly toasted, around 3 minutes. Season with salt and pepper, then set aside to cool slightly.
Transfer the bread crumb mixture to a large mixing bowl. Add the Parmesan, cream cheese, parsley, and thyme. Season again with salt and pepper, and mix until everything is well combined. Spoon the filling into the mushroom caps, mounding it slightly. Sprinkle with additional Parmesan for a crisp, golden topping.
Bake the mushrooms in the preheated oven for approximately 20 minutes, or until the mushrooms are tender and the tops are a beautiful golden color.
Carefully transfer the stuffed mushrooms to a serving platter and garnish with a bit of fresh parsley for added color. Enjoy warm.