To bake the spaghetti squash: Preheat oven to 400 F. Option to line a rimmed baking sheet with parchment paper. Cut the squash in half lengthwise with a sharp knife -- if you're having trouble getting through the stem, you can slice that off. Place the squash cut side down on your prepared baking sheet and bake in the preheated oven until the flesh is tender enough to flake with a fork, about 30 minutes. (Psst--overcooking the squash can make this dish mushy, we like our spaghetti squash slightly al dente). Scoop the seeds out with a spoon and discard. Then shape the spaghetti using a fork.To microwave the squash: Pierce the flesh of the squash all over with a fork. Microwave on high for 5 minutes, flip and microwave the other side for another 5 minutes. Let the squash sit on the counter for at least 5 minutes before slicing in half, removing the seeds, and flaking the noodles.Keep the spaghetti squash bowls on a plate and set aside. Keep spaghetti squash warm by placing foil over the top.
Melt 4 tablespoons of butter in a large skillet over medium heat. Add the shallot 1/2 teaspoon of salt and 1/4 teaspoon of pepper and saute until soft, about 3-4 minutes. Add the garlic and red pepper flakes and continue to cook until fragrant, about 2 minutes.
Add the shrimp and sprinkle with 1 teaspoon salt and 1/4 teaspoon pepper. Continue to cook until the shrimp are golden pink and cooked through, about 2 minutes per side.
Add the white wine, and scrape up any brown bits from the bottom of the pan. Add lemon juice, and lemon zest and simmer until slightly thickened. Remove from heat, and stir in 2 additional tablespoons of butter and parsley.
Add spaghetti squash to your pan and toss to coat in the sauce. Scoop into the squash boats, top with additional parsley, red pepper flakes, and parmesan, and enjoy!