Heat oven to 450°F. Bake potatoes on racks until fork-tender and skins are crisp, 45–50 minutes.
Toss butternut squash with 1 tablespoon olive oil and season with salt and pepper, arrange in a single layer on a baking sheet; set aside.
Remove potatoes from oven, immediately halve, and scoop out flesh. Decrease oven to 400°F and roast squash until fork-tender, about 15 minutes, stirring halfway through.
Meanwhile, weigh out 1 pound potato flesh and press through a ricer into a large bowl; let cool 5 minutes. Using a fork, gently stir in egg just until combined. Sift all-purpose flour, buckwheat flour, salt, pepper, and nutmeg over potato mixture and gently combine with fork just until no pockets of dry flour remain.
Gently press mixture together then transfer to a lightly floured surface and gently knead until dough is slightly sticky and smooth, about 1 minute.
Line two baking sheets with parchment paper and dust liberally with flour. Cut dough into 8 pieces then roll each piece into a ½-inch-thick rope. Cut ropes into ¾-inch-long pieces, and using the back of a fork, press each piece of dough, cut side down, against tines of fork with your thumb, roll down and off the fork to form ridges and indentation. Transfer gnocchi pieces to prepared baking sheets and repeat with remaining dough.
Bring a pot of salted water to a low boil. Meanwhile, get your sauce of choice started.
For an olive oil sauce: Heat 1 tablespoon oil in a large nonstick skillet over medium-high, add shallots and cook 1 minute, add garlic, sage, and thyme and cook until fragrant, about 30 seconds; remove from heat and cover to keep warm.
For a browned butter sauce: Heat butter in a large nonstick skillet over medium heat and cook, swirling, until it starts to brown and become fragrant. Add shallots, garlic, sage and thyme and cook until fragrant, about 30 seconds; remove from heat and cover to keep warm.
Using parchment paper as a sling, slide half of the gnocchi into pot of moderately boiling water, and cook until firm and just cooked through, 90 seconds (gnocchi should float to the top after 1 minute). Using a spider or slotted spoon, remove gnocchi and transfer to skillet with sauce, cover to keep warm then repeat with remaining gnocchi. Add roasted squash to skillet with gnocchi and gently toss to combine with, serve with Parmesan and additional herbs.