Preheat the oven to 350°F (175°C) and line a baking dish or rimmed baking sheet with parchment paper.
Juice 1 blood orange into a large mixing bowl.
Add the balsamic vinegar, soy sauce, molasses, honey, minced garlic, halved onions, ground ginger, paprika, kosher salt, and melted coconut oil to the bowl; whisk until smooth.
Add the chicken thighs to the bowl and toss or rub the glaze over each piece so they are well coated.
Place the coated chicken in the prepared baking dish in a single layer and pour any remaining glaze over the chicken.
Slice the remaining blood orange and arrange the slices in the dish with the chicken, then tuck the radishes and thyme sprigs around the chicken.
Bake for about 20 minutes, turning the chicken once halfway through the cook time to promote even browning.
Remove from the oven, season with ground black pepper to taste, and serve with any pan juices or reserved glaze.