In medium saucepan, bring stock, water, nutmeg, ginger, 1 teaspoon kosher salt, cloves and cinnamon stick to boil. Add rice and bring back to simmer. Reduce heat to low and half cover with lid. Allow rice to simmer about 45 minutes, or until tender and liquid is absorbed. Remove and discard cinnamon stick.
While rice is cooking, in large skillet, heat olive or pecan oil and butter. Add onion and cook, stirring frequently, until translucent, about 4 minutes. Add in butternut squash and cook, stirring often, until squash is tender and beginning to caramelize at edges, about 8-10 minutes. Add in apples and cook additional 3-4 minutes, or until apples soften. Season with salt and pepper, to taste, along with thyme and ground cinnamon. Stir in chopped pecans and currants, and cook until pecans are slightly golden and fragrant. Remove mixture from heat.
Stir butternut squash mixture with cooked rice and season, to taste, with salt and pepper. Serve warm or at room temperature.