Preheat the oven to 500 degrees Fahrenheit with a pizza stone inside of it. For the shallot pear sauce, melt the butter in a medium skillet over medium low heat. Add the shallot and saute until softened and translucent, about 5 to 7 minutes. Add the pear and sautee until the shallots turn lightly golden, about an additional 15 to 20 minutes more, stirring every 5 minutes. Remove from heat and allow to cool for 10 minutes before pureeing in a blender or food processor.
For the sherry caramelized onion topping, melt the butter in a medium skillet over medium low heat. Add the onions and stir to coat in the mixture. Continue cooking until the onions for an additional 20 minutes, stirring every 5 minutes. Add the cream sherry and stir to incorporate. Reduce heat to low and continue cooking until the onions are lightly golden, about 15 to 20 minutes more, stirring every 3 to 5 minutes. Remove from heat and set aside.
For the honeyed pear topping, heat the water and honey in a medium frying pan and bring to a low boil over medium heat. Add the pear slices and stir gently to coat in the syrup. Continue cooking until the mixture is bubbly and the pears are golden in color, about 10 to 15 minutes. Strain and set aside, reserving the honeyed pears.
Using lightly floured hands, spread out the pizza dough on a lightly floured working surface using your fingertips to push the edge of the dough ball out into a roughly circular or oval shape. Transfer the shaped crust to a sheet of parchment paper on a flat baking sheet. Spread the pear and shallot puree onto the crust with a rubber spatula, leaving 1-inch bare around the edge for the crust. Top with the sherry caramelized onion, honeyed pears, prosciutto, and bonne bouche.
Open the oven and pull out the rack with a baking stone. Hover the baking sheet over it and pull the parchment paper with the pizza on it off, sliding it onto the hot stone. Push the rack with the stone back into the oven and close the door. Bake until the crust is golden and the toppings are bubbly and lightly golden at the edges, about 15 minutes. Remove from the oven and allow to cool for 5 minutes before topping with the fresh thyme leaves, slicing, and serving.
Tip: Use kitchen shears to cut the pizza instead of a pizza wheel!