In a medium bowl, whisk together flour and salt. Pour the flour mixture out onto a clean surface. Using your hands, make a well in the center of the flour. Crack eggs into the well and use a fork to slowly whisk the flour into the eggs until a shaggy dough forms. Use your hands to knead the dough until smooth and no longer sticky, about 5 minutes. Add flour to the surface as necessary to keep the dough from sticking. Wrap the dough tightly in plastic wrap and refrigerate for at least 1 hour.
Meanwhile, make the filling: Drain the pumpkin by placing it in a fine mesh strainer set inside a large bowl. Cover the exposed pumpkin with plastic wrap, then place a small bowl on top to lightly press the pumpkin. Let drain for 15 minutes.
When the pumpkin has drained, transfer it to a medium bowl. Add Parmesan, egg yolk, sugar, and nutmeg, then season with salt and pepper. Stir to combine.
When ready to roll the pasta, cut the dough into quarters. Wrap all but one piece back in plastic wrap and place it back in the refrigerator.
On a lightly floured surface, roll the uncovered dough into a long rectangle about 1/4 inch thick. Set the pasta maker to the widest setting and pass the rolled-out dough through twice. Fold the short ends of the dough to meet in the center of the rectangle, then fold in half so that the dough is in quarters. Roll out again so the dough is 1/4 inch thick, then pass through the pasta maker two more times.
Reduce the setting by one degree. Repeat the process of rolling and folding 2 to 3 times before going to the next setting. Repeat this process all the way to the thinnest setting. If your pasta sheet becomes too long to work with, cut it in half. Repeat with the remaining dough in the refrigerator. Keep the rolled-out dough covered with a clean kitchen towel.
Lay one piece of dough out on a lightly floured surface. Spoon about 1 tablespoon of filling every 1 inch. Using your finger, lightly wet between each pile of filling with water. Gently lay a second piece of dough on top and press between filling to seal, making sure to press out as much air as possible. (Air trapped in the ravioli will force them to the surface when boiling.) Using a biscuit cutter or knife, cut between each pocket to make individual ravioli. If desired, use fork tines to seal the ravioli shut. Repeat with the remaining dough and filling. Refrigerate until ready to cook.
When ready to serve, melt butter in a medium skillet. Add pumpkin seeds and cook, swirling the pan occasionally, until the pumpkin seeds are toasted and the butter is browned and smells nutty, 6 to 8 minutes. Add garlic and thyme and cook until fragrant, 1 minute more, then remove the pan from heat.
In a large pot of boiling salted water, working in batches, add ravioli and cook until tender, about 1 ½ minutes. Use a spider to remove them from the water and place directly in the brown butter. Gently toss to coat. Serve warm with Parmesan.