Line rimmed baking sheet with parchment paper. Combine flour, 6 tablespoons butter, sugar, baking powder, and salt in food processor and process until butter is fully incorporated, about 15 seconds. Add cheddar and remaining 6 tablespoons butter and pulse until cheddar and butter are reduced to pea-size pieces, 10 to 12 pulses. Transfer mixture to large bowl. Stir in jalapeños until coated with flour mixture.

Beat milk and egg and yolk together in separate bowl. Make well in center of flour mixture and pour in milk mixture. Gently stir mixture with rubber spatula, scraping from edges of bowl and folding inward, until very shaggy dough forms and some bits of dry flour remain. Do not overmix.

Turn out dough onto well-floured counter and knead briefly until dough just comes together, about 3 turns. Using your floured hands and bench scraper, shape dough into 15 by 3-inch rectangle with long side parallel to edge of counter, dusting with extra flour if it begins to stick.

Using knife or bench scraper, cut dough crosswise into 6 equal rectangles. Cut each rectangle diagonally into 2 triangles (you should have 12 scones total). Transfer scones to prepared sheet, spacing about 1 inch apart. Cover sheet with plastic wrap and refrigerate for at least 30 minutes or up to 24 hours. Adjust oven rack to middle position and heat oven to 425 degrees.

Meanwhile, combine melted butter and honey in small bowl.

Uncover scones and bake until lightly golden on top, 15 to 17 minutes, rotating sheet halfway through baking. Remove scones from oven and brush tops with honey butter. Return scones to oven and continue to bake until golden brown on top, 3 to 5 minutes longer. Transfer scones to wire rack and let cool for at least 10 minutes before serving.