Preheat the oven to 200°C (180°C fan). Toss the butternut squash cubes in olive oil, salt, pepper, and thyme, if using. Roast for 25–30 minutes, turning once, until caramelized at the edges and tender throughout. Set aside. Purée two-thirds of the squash for stirring into the risotto and keep the rest whole for serving.
Blend the toasted pumpkin seeds, herbs, garlic, cheese, lemon zest, salt, and olive oil into a loose pesto. Add a touch more oil if needed. Taste and adjust for salt or acidity.
In a Sautese pan, heat the olive oil and butter over medium heat. Add the chopped onion and cook gently for 5–7 minutes until soft and translucent. Stir in the garlic and rice, coating the grains until they begin to turn pearlescent.
Pour in the Cognac and let it bubble away, stirring gently, until the alcohol has evaporated and the scent becomes mellow and warm.
Begin adding the warm stock a ladle at a time, stirring constantly and waiting until each addition is absorbed before adding the next. This will take about 18–20 minutes. The rice should be tender with a slight bite and suspended in a creamy liquid.
Stir in the squash purée and grated cheese. Add a knob of butter for silkiness. Taste for seasoning. Let the risotto rest, covered, for 2 minutes before serving. Meanwhile, fry the thyme blossom sprigs in a little oil until crisp.
Spoon the risotto into warm bowls. Top with extra roasted squash cubes, a generous drizzle of pumpkin seed pesto, the fried thyme blossom and a few toasted seeds for crunch.