Preheat oven to 350 degrees. Coat 2 standard muffin tins with cooking spray, dust with flour, tap out excess. Sift flour, granulated sugar, baking soda, baking powder, and salt into a mixer bowl. Add egg, yolk, water, buttermilk, oil, and vanilla to bowl; beat on low speed until smooth, about 3 minutes.
Divide batter among 20 muffin tins, filling each cup about 2/3 full. Bake, rotating tins halfway through, until cupcakes are golden brown and a tester inserted into centers comes out clean, about 17 minutes. Let cool in tins placed on wire racks for 15 minutes, then turn cupcakes out onto racks, and let cool.
Beat cream cheese, butter, and confectioners' sugar with a mixer on medium-high until smooth. Beat in milk and vanilla.
Spoon 2 tablespoons jam into the bottom of each jar. Place cupcake on top, then top with 2 tablespoons frosting. Cupcakes can be stored for 1 day.
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