Sieve salt and pepper into flour and rub onto both sides of pork chops, shaking off any excess. Heat margarine in a large frying pan over medium high heat. Brown chops on both sides, reducing heat if necessary and working in two batches depending on the size of your frying pan. Remove from heat and set aside.
Peel squash and slice crosswise into 3mm thick slices. Arrange half of the slices in the bottom of a baking dish. Place pork chops over squash and top with remaining slices.
Melt butter in a small saucepan over medium heat. In a bowl, stir remaining 2 tablespoons flour and 1/4 teaspoon salt together with ginger and thyme; add to butter and stir. Cook for 3 minutes, then very gradually whisk in chicken stock, avoiding any lumps. Continue to cook and stir until slightly thickened, then stir in onion. Pour over chops and squash and cover with foil.
Bake in the preheated oven for 45 minutes or until squash is tender and pork is no longer pink inside.
If acorn squash is unavailable, use butternut squash instead.