Preheat the oven to 375°F. Grease a 9 x 12 baking dish, set aside.
In a small saucepan, heat honey and 1/2 tsp thyme, stirring occasionally over low heat for 3-4 minutes. Set aside.
In a large microwave-safe dish, place the squash and water. Cover with plastic wrap and microwave on high until the squash is just tender, about 6 minutes. Drain. Add vegetable oil, 1 tsp each salt and pepper. Toss to coat.
Arrange squash slices by stacking in greased baking dish. (Tip baking dish on it's side to make stacking the squash slices easier.) Drizzle 1/4 cup of the honey mixture over the squash.
Bake until squash is fully tender, 45-50 minutes.
In a small skillet, melt butter over medium heat. Add panko, and remaining thyme, salt and pepper. Cook and stir until panko is golden brown, about 5 minutes. Sprinkle over baked squash and drizzle remaining honey mixture over the top.