Preheat your oven to 425°F (220°C). Grease a muffin tin and set aside.
In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.
Add the freshly milled flour, salt, cinnamon, nutmeg, cloves and allspice to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.
While resting the batter, make the streusel topping (if desired) by combining the flour, sugar, cinnamon, salt and cold butter. Use a fork or your fingers to bring it together into a dry, crumbly mixture. Set aside.
After resting, sprinkle the baking powder and baking soda into the batter. Mix gently until everything is evenly combined, being careful not to overmix.
Toss the diced apple slices in the tablespoon of flour, until coated. This will help the fruit not sink to the bottom. Fold the apples into the batter.
Working quickly, spoon the batter into the prepared muffin tin, filling each cup evenly.
If adding the streusel topping, sprinkle over each muffin, gently pressing the crumbs into the batter.
Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 7-9 minutes, or until the centers feel firm and the muffins are baked through.
Remove from the oven and let cool slightly on a wire rack.