Combine butter and cream cheese: To the bowl of a stand mixer fitted with a paddle attachment, add the butter and salt. Add the cream cheese in large pieces and mix on medium-low speed until combined.
Make the dough: Turn off the mixer, add the flour and over low speed mix until the dough is shaggy and has a few dry spots but starts to gather around the paddle into a ball, should take about 1 minute. Use a rubber spatula to transfer the dough to a large piece of plastic wrap. Fold the plastic wrap over the dough and use the plastic wrap to help shape the dough into a 1-inch-thick rectangle. Wrap the dough tightly in plastic wrap and refrigerate for at least 2 hours.
Make the filling: Add the poppy seeds to a small sauce pan along with the honey, water, lemon zest and juice, orange zest, and salt, over medium-low heat. Stir the mixture together and cook until the mixture thickens slightly, about 10 minutes. Transfer the mixture to an airtight container and refrigerate until completely chilled, about an hour.
Roll the dough: Lightly flour your work surface, remove the plastic wrap from the chilled dough and place it on your work surface. Sprinkle a bit of flour over the top of the dough and roll it into a ¼-inch-thick rectangle with the short end facing you. Use a pastry brush to remove any excess flour from the top of the dough, then fold the dough into thirds like a business letter. Roll the dough again until it's ¼-inch-thick, and fold like a letter. Repeat this step one more time. Cut the dough into 3 pieces and wrap each piece of dough in plastic wrap. Chill for 1 hour.
Preheat the oven: Preheat oven to 350°F.
Prepare the topping: In a small bowl, stir together the sugar, cinnamon and nutmeg; set aside.
Assemble the cookies: Lightly flour the work surface and roll out a piece of the chilled dough into a 12-inch circle. Place a 12-inch cake pan or a lid over the dough and cut around it, to end up with a perfect circle. Lightly moisten the edge of the dough (about ½ inch around the perimeter) with water and dollop ⅓ of the poppy seed filling over the surface of the dough. Using a spatula spread the filling into an even layer that just reaches the about ½-inch from border.
Roll the cookies: Use a pizza cutter or sharp knife to divide the circle into quarters. Slice each quarter into 3 so that you have 12 small triangles. Starting at their wide ends, roll up each triangle. Place the rugelach cookies on a baking sheet so the small tip is on the underside of the rugelach. Repeat with the remaining triangles. Repeat with the remaining pieces of dough and filling.
Finish: Sprinkle the cookies with the spiced sugar. Bake until the rugelach are nicely browned, about 30 minutes. Allow the cookies to cool on the baking sheets for 10 minutes before transferring to a wire rack to cool completely.