Pour 3 cups water into a large saucepan and bring to a simmer. Add the green beans and simmer for 3-4 minutes, until they are bright green. Remove and set aside.
Discard water from the pan.
For the Casserole
In the same large sauce pan, melt butter. Add the flour, salt, pepper, onion powder, garlic powder, thyme, and sage. Cook for 1-2 minutes.
Add the milk and whisk until combined.
Simmer until slightly thickened, about 2 minutes.
Add chopped green beans and stir until combined.
For the Topping
Melt 2 tablespoons of the butter and stir in the panko and shallot.
Sprinkle over the top of the green beans.
Bake for 15-18 minutes, or until the top is golden brown and the sides are bubbly.