In a small saucepan, whisk the milk, cornstarch, thyme, garlic powder, salt, and pepper over medium heat and bring to a boil, whisking constantly. Reduce the heat slightly and simmer until slightly thickened, 4 to 6 minutes. Remove from heat and stir in the Parmesan cheese until smooth.
Preheat the oven to 350 degrees F. Spray 6 8-ounce ramekins with cooking spray and place them on a large rimmed baking sheet.
Divide half of the potato slices among the ramekins, laying them flat and making sure that they are spread out to the edges of the ramekin (not all in one single stack). Pour half of the Parmesan sauce evenly over the potatoes, sprinkle half of the cheddar among the ramekins, then repeat with the remaining half of the potatoes, sauce, and finish with the cheddar.
Cover each ramekin with foil and bake until the potatoes are beginning to soften and the sauce is bubbling, 30 to 35 minutes. Remove the foil, increase the oven temperature to 425 degrees F, sprinkle the tops evenly with the remaining cheddar and bake until the potatoes are tender, about 15 minutes.
Use a butter knife and run it around the inner edge of each ramekin and let them cool for 10 minutes. Sprinkle the tops evenly with the fresh chives and serve.
Nutrition Information for 1/8th of the Recipe: Calories 173.6, Total Fat 7.5g, Sat Fat 4.7g, Cholesterol 24.4mg, Carb 17.8g, Fiber 2g, Sugars 2.5g, Protein 8.7g