To make the pizza dough, stir the water, honey, and yeast in a medium bowl to combine. Cover and set aside for 5-10 minutes until foamy.
Add 3 cups of the flour, 3 tablespoons of the olive oil, and all of the salt to the bowl. Stir until a shaggy dough forms.
Sprinkle ¼ cup of flour onto a clean surface and place the dough on top. Knead for 6-8 minutes until combined and smooth, adding the remaining ¼ cup of flour as needed if it's too sticky. Shape the dough into a ball.
Coat a medium bowl with the remaining olive oil, place the dough ball inside, and turn the dough in oil to coat.
Cover the bowl of dough and set aside to rise for 1-1 ½ hours until doubled in volume. (Or, refrigerate for up to 3 days if you're making the dough ahead of time.)
To make the filling, heat the olive oil in a large pot over medium heat until shimmering.
Add the sausage and break apart with a wooden spoon.
Add the bell pepper and onion and cook for 5-7 minutes, stirring occasionally until browned.
Add the garlic and cook for an additional minute, then season generously with salt and pepper to taste.
Add the crushed tomatoes, oregano, and sugar to the pot. Cook the sauce uncovered over low heat, stirring occasionally, for 25-30 minutes until thickened.
Stir in the basil and season with additional salt and pepper as needed. Remove the pot from the heat and set aside if using right away, or refrigerate until ready to use.
To assemble the pot pies, preheat the oven to 475 F and line a baking sheet with parchment paper.
Lightly dust a clean countertop with flour, place the dough on top, and divide it into 8 even pieces.
Roll or stretch each piece into a 6-inch round, dusting with flour as needed to prevent sticking.
Transfer the discs to the prepared baking sheet, placing a sheet of parchment between the layers. Set aside.
Brush the interior and edges of eight 8-ounce ramekins with about ½ of the melted butter.
Place 3 mozzarella slices in the bottom of each ramekin, followed by 4 mushroom quarters and 1 tablespoon of Parmesan per portion. Finally, ladle about ½ cup of tomato sauce into each ramekin.
Top each serving with a round of pizza dough, pressing lightly along the edges to adhere. Leave about 1 inch of overhang on all sides, trimming any excess dough if needed.
Place the ramekins onto a baking sheet and bake for 14-16 minutes until deeply golden brown.
Remove the pot pies from the oven and, while hot, brush the tops with the remaining melted butter.
To serve, carefully use tongs or a kitchen towel to flip each ramekin onto a plate. Run a spoon around the edges to loosen the contents, then lift the ramekins to reveal the pot pies.