Preheat the oven to 400 degrees F (200 degrees C). Line a large baking sheet with parchment paper.
Place the cubed squash and whole garlic cloves on the prepared baking sheet. Drizzle with olive oil, sprinkle with half of the salt and black pepper, and toss to coat evenly.
Roast in the preheated oven for 40 to 45 minutes, or until the squash is very fork-tender and lightly caramelized at the edges.
Transfer the roasted squash and garlic into a large mixing bowl or food processor.
Add the warmed almond milk, melted vegan butter, fresh thyme, and remaining salt and black pepper.
Blend using an immersion blender, food processor, or potato masher until creamy and smooth.
Fold in the chopped fresh chives, taste for seasoning, and serve hot.