Whisk the flour and salt in a 3-quart / 2.8 L bowl. Rub in the cold butter with your fingertips until the pieces are flat flakes the size of almonds. Add the ice water 1 tbsp at a time until the dough clumps when squeezed, pat it into a 2.5 cm / 1-inch disk, wrap it, and chill for 30 minutes.
While the dough chills, heat the oven to 220 C / 425 F. Toss the squash and onion wedges with 1 1/2 tbsp of the olive oil, the salt, and the pepper on a parchment-lined sheet pan, 33 x 46 cm / 13 x 18 inch, in a single layer. Roast for 20 minutes, stirring once at the 10-minute mark, until the edges are browned and a fork slips in easily.
Tip the squash and onion into a bowl, toss with the thyme, and let cool for 10 minutes. Meanwhile, lower the oven to 200 C / 400 F, move a rack to the lower third, and roll the chilled dough on a lightly floured sheet of parchment into a 30 cm / 12-inch round about 4 mm thick. Slide the parchment onto a second, cold sheet pan, 33 x 46 cm / 13 x 18 inch.
Spread half the goat cheese (60 g) over the dough, leaving a 4 cm / 1.5-inch border. Pile the cooled squash and onion on top and dot with the remaining goat cheese. Fold the border over the filling in loose pleats, pinch any cracks closed, and brush the crust with the egg wash.
Bake for 30 minutes, until the crust is starting to turn golden. Toss the sage leaves with the remaining 1/2 tbsp oil, scatter them over the filling, and bake 10 minutes more, for 40 minutes total, until the crust is deep golden and the goat cheese is browned in spots.
Cool on the pan for 10 minutes so the cheese sets. Drizzle with the honey and cut into 6 wedges.