Preheat the oven to 425 degrees F. Line a baking sheet with parchment paper.Heat 1 tablespoon olive oil in a large skillet over medium-high heat. When the oil shimmers, add the onions and honey and cook 5 minutes, stirring occasionally until softened. Season with salt and pepper and continue cooking another 5-10 minutes or until the onions are golden and caramelized. Add the garlic, and thyme, cook another minute. Remove from the heat.In a bowl, combine the remaining 1 tablespoon olive oil, the tomatoes, balsamic vinegar, basil, crushed red pepper, and a pinch each of salt and pepper. Lay the pastry sheet flat on a clean, floured surface. Gently roll the sheets out to stretch slightly. Cut each sheet into 4 squares and place onto the prepared baking sheet. Evenly top each square with onions, leaving a 1/4 inch border. Top with both kinds of cheese and then mound the tomatoes over the cheese, pressing them into the cheese to adhere slightly (see above photo). Fold the edges of the pastry inward to enclose the tomatoes. Brush the edges of the pastry with beaten egg and sprinkle with everything spice. Transfer to the oven and bake for 20-25 minutes or until the pastry is golden and the tomatoes burst. Top with fresh thyme and chives.