Preheat oven to 350°.
To prepare crust, lightly spoon 1/2 cup flour into a dry measuring cup; level with a knife. Combine with wheat germ and brown sugar in a small bowl; cut in margarine with a pastry blender or 2 knives until well-blended. Press mixture into a 9-inch square baking pan coated with cooking spray. Bake at 350° for 15 minutes. Cool on a wire rack.
To prepare filling, combine granulated sugar, 2 tablespoons flour, and baking powder in a medium bowl. Add cream cheese and eggs; beat at high speed of a mixer until well-blended. Stir in rind and juice. Spread filling over crust. Bake at 350° for 25 minutes or until filling is set. Cool on a wire rack. Spread whipped topping evenly over filling.