Place a pizza stone on the middle rack of the oven and preheat the oven to 500 degrees F.
In a medium size saute pan, add olive oil and heat over medium heat. When the oil is hot, add the bacon and cook until the bacon is very crispy and all of the fat is rendered. Remove the bacon with a slotted spoon and drain on a paper towel-lined plate. Remove all but 2 tablespoons of the bacon fat from the pan and discard. Place the pan over high heat. Add the onions to the hot bacon fat and cook until the onions are well browned, about 8 to 10 minutes, stirring often. Remove to a paper towel lined plate.
In a small bowl, combine the mascarpone and farmer's cheeses. Season with nutmeg and black pepper. Reserve.
On a lightly floured surface, stretch or roll the dough as thinly as possible, about 14 to 15-inch circle. Evenly spread the mascarpone mixture over the dough. Sprinkle with the mozzarella and Parmesan cheeses, bacon, thyme, and sauteed onion. Bake until the pizza crust is nicely browned, about 8 to 10 minutes.
Remove pizza from the oven, transfer to a cutting board, cut into slices and serve immediately.
In a small bowl, dissolve the yeast and honey in 1/4 cup warm water.
In a food processor, combine the flour and the salt. Add the oil, the yeast mixture, and the remaining 3/4 cup of water and process until the mixture forms a ball. (The pizza dough can also be made in a mixer fitted with a dough hook. Mix on low speed until the mixture comes cleanly away from the sides of the bowl and starts to climb up the dough hook).
Turn the dough out onto a clean work surface and knead by hand 2 or 3 minutes longer. The dough should be smooth and firm. Cover the dough with a clean, damp towel and let it rise in a cool spot for about 2 hours. (When ready, the dough will stretch as it is lightly pulled).
Divide the dough into 4 balls, about 6 ounces each. Work each ball by pulling down the sides and tucking under the bottom of the ball. Repeat 4 or 5 times. Then on a smooth, unfloured surface, roll the ball under the palm of your hand until the top of the dough is smooth and firm, about 1 minute. Cover the dough with a damp towel and let rest 1 hour. At this point, the balls can be wrapped in plastic and refrigerated for up to 2 days.