Preheat the oven to 425 degrees F. Line 2 sheet pans with parchment paper.
In a medium saute pan, cook the bacon over a medium-low heat until it begins to render, 3 to 5 minutes. Add the onions and cook until they begin to soften, about 3 minutes. Season with pepper. Set aside to let cool. Add the thyme to the cooled bacon-onion mixture.
In a bowl, combine the farmer's cheese, creme fraiche, egg yolk and salt and pepper to taste. Set aside.
Flour a flat surface and place the puff pastry on top. Flour the top and gently roll into a 13-by-18-inch rectangle. Cut the pastry in half and transfer each to a lined sheet pan. Using a fork, dock the puff pastry (pierce it slightly with the tines), leaving a 1-inch border untouched.
Divide the cheese mixture between the two sheets of pastry and spread evenly on the docked area. Top each tart with half of the bacon-onion mixture.
Place the tarts in the oven on the lower racks and bake, rotating halfway through, until the crusts are dark golden, about 25 minutes. Garnish with the pecorino and chives.
Be sure to roll out the puff pastry very thin so that it stays thin while it bakes.