Preheat oven to 400°F (200°C) and line a large baking sheet with parchment paper.
Toss diced butternut squash with 2 tablespoons olive oil, 1 tablespoon honey, salt, pepper, and 1 teaspoon fresh thyme. Spread into an even single layer.
Roast for 22 to 25 minutes, tossing halfway through, until fork-tender with caramelized golden edges.
In a food processor, blend goat cheese, heavy cream, minced garlic, and a pinch of salt until light, creamy, and spreadable (1-2 minutes).
Arrange baguette rounds on a baking sheet, brush lightly with remaining olive oil, and bake at 400°F for 7-9 minutes until golden and crisp.
Generously spread whipped goat cheese over each toasted crostini.
Top with warm roasted butternut squash cubes, pressing gently to adhere.
Sprinkle with toasted chopped pecans and pomegranate arils. Drizzle remaining tablespoon of honey, scatter fresh thyme leaves and flaky sea salt, and serve!